Coming from a Lian Li A3-mATX, which has been a great case but I want to go even smaller. Case and a few accessories are already ordered; everything else is still open, including the motherboard. I do a lot of work that loads the CPU and GPU hard at the same time, so thermals under simultaneous load matter more to me than acoustics.

Current components (all carrying over except possibly the mobo):

• GPU: PNY RTX 5090 ARGB Epic-X OC (328.7 × 137.7 × 71 mm, 3.5-slot)
• CPU: Ryzen 9 9950X3D (~200-230 W package power all-core in my logs)
• PSU: ASUS ROG Loki SFX-L 1200W Titanium (125 × 125 × 63.5 mm)
• SSD: Samsung 9100 PRO 2TB with heatsink (25 mm wide)
• RAM: Corsair Vengeance 2×32 GB DDR5-6000 CL30 EXPO
• mATX Motherboard: MSI MAG B850M Mortar WiFi (happy to replace this if an ITX board makes the build meaningfully better)

Already ordered from NCASE:

1. M2 Grater Flatpack Kit, 2× Mesh Side Panel / Silver + Gray Dust Filter
2. Screws + Fittings, M2 + M3 + S5M + T1 Screw Kit / Black
3. Power Supply Inlet Cable, Left Angled

What I can't figure out

I've gone through M2 Build Levels 5 through 8 and I can't work out which one my parts should actually follow. None of them specify a CPU, and none publish any temperature data, so I can't tell what the thermal consequences of each config actually are for a 600 W card plus a 200 W+ CPU in the same volume.

Specifically:

1. Classic vs Flipped? From what I understand Flipped puts the GPU against the top panel instead of the bottom, which seems like the better place for a card that has to breathe passively (just using the GPU's fans). But Classic seems to be what most ITX builds run. Which one would you pick for a 3.5-slot 5090 that's going to sit at 600 W for hours?

2. Do I keep the mATX board or buy an ITX one? My read is that mATX eats the tray's 5 mm vertical adjustment and closes off the top/bottom fan positions. Level 8 is mATX and lists only the two radiator fans, which suggests there's nowhere else to put a fan with a 244 mm board in there. If that's right, an ITX board buys me actual case fans and tray adjustment for the GPU clearance. Is that worth ~$350-450 to you, or is it fine to run a 280 rad as the only active cooling?

3. Which AIO? I've seen a comment claiming an Arctic Liquid Freezer III 280 fits on the side mesh bracket if you pull the magnetic VRM fan and mount the block upside down on the CPU. Can anyone confirm that with a 38 mm radiator? If not, is a 27-30 mm standard radiator the safer call, and how much does it actually cost me thermally on a 9950X3D?

4. Case fans? Depends on the answer to #2, but I'd like to know what positions are genuinely usable in each config, and whether slim 120s on the bottom are worth it. I already own a few Arctic P12 Slims.

Happy to provide anything else that would help such as exact clearances, photos, whatever. Thanks in advance.

UPDATE (Aug 18): everything's ordered. Motherboard and AIO are settled; Classic vs Flipped is the only thing still open.

Build:
Case: NCASE M2 Grater (flatpack, 2× mesh)
GPU: PNY RTX 5090 Epic-X OC (328.7 × 137.7 × 71 mm, 3.5-slot, axial, not flow-through, 600 W)
CPU: 9950X3D (200–230 W all-core)
Motherboard: MSI MPG X870I Edge Ti EVO
AIO: Noctua NL-LC1-24
PSU: Loki SFX-L 1200 W
RAM: 64 GB DDR5-6000 CL30
SSD: 9100 PRO 2 TB with Heatsink
Cables: Cablester custom 24-pin + 8-pin EPS
Riser (Instead of taller case feet): 64 mm riser stand

What this thread settled

AIO: Noctua NL-LC1-24. Noctua's compatibility page lists it as M2-compatible 279.5 × 120 × 30 mm, 59 mm assembled stack. At 279.5 mm it also dodges the length clash a 280 runs into with a 125 mm SFX-L. Hardware Canucks measured it at 82 °C on a 250 W 9950X noise-normalised to 32 dBA, beating 360s at that noise level. Also this post shows that it fits on the side mount.

The Arctic LF III is out: on tube stiffness and congestion, not radiator thickness. A 9950X3D in an M2 with an LF3 280 and T30s at 3000 rpm sits at 92-93 °C; the builder in this post couldn't move the fans to the side bracket without kinking the tubes, and pulling the rad out of the case dropped him 13 °C.

Radiator inlet air temperature is the dominant variable. My A3 logs: ~0.85 °C of Tctl per 1 °C of inlet air, ~8.8 °C going from room air to case air. GamersNexus measured ~5-6 °C for the same effect in a 41 L mid-tower, so an SFF case with a 600 W card being worse tracks.

A 3.5-slot card eats every fan position. Roughly 80 mm of vertical budget against 71 mm of GPU leaves ~9 mm, so no top fan in Classic, no bottom fan in Flipped, not even a 15 mm slim. The side bracket is the AIO; the rear is the only position left (NCASE spec: 1× 92 mm). Under-GPU fans are a VGPU feature, not a Classic option. This is also the real reason I went ITX, not fan count. With a thick card that vertical budget goes to the GPU either way; ITX buys tray adjustment and cable room.

Nothing at the rear is native: no factory screw pattern, no manual step, no NCASE STL. What people actually do: NF-A9 held by a Noctua NA-FD1 spacer kit (rhialto.com/ncase-m2); NF-A9x14 slim; a printed 90 mm bracket needing 20-30 mm M3 bolts (Thingiverse 7036754); or a 120 mm NF-A12x15 on a printed mount (MakerWorld 1016234, designed for a vertical-GPU build). Usable rear width is ~121 mm after the ITX I/O shield, which is why 120s have to be slim.

VGPU is out on CPU thermals while being the best or near-best for GPU thermals vs Classic and Flipped.

Still open: Classic vs Flipped for a thick axial card

The one measured M2 config comparison (Chris Russell Tech) found Classic best, up to 12 °C on the CPU in 4K Cyberpunk, but he attributes the flat GPU results to the 5080 FE's flow-through design, and his configs used supplementary fans. Bottom fans not possible for my 71mm thick GPU.

Classic: GPU breathes the bottom panel through the riser and exhausts sideways. The rad sits above it but can't physically overlap it, and as intake against a mesh panel it pulls room air rather than re-breathing case air.

Flipped: GPU exhaust leaves through the top of the side panel instead of rising past the rad, but the card is then intaking where hot air collects, which is what the M3 "heat cushion" report in this thread describes. Worth noting everyone here with an M2 said Classic; both inverted recommendations came from M3 owners, which has bottom-fan room my card takes away in an M2.

What I'm asking:

1. Has anyone run a thick axial (non-flow-through) 4090/5090 in an M2 in both (Classic and Flipped) configs? I can't find this comparison anywhere.
2. Rear fan as intake or exhaust? Two M2 owners here run it as intake. With an AIO it isn't feeding a heatsink, it's ventilating the board zone, and it's the only outlet when the rad and the GPU are both pulling in. Has anyone actually A/B'd it?
3. Has anyone fitted a 120 mm at the rear in Classic or Flipped (rather than a vertical-GPU build), and did it clear the side radiator bracket?

Plan unless someone talks me out of it: Classic, 240 as side intake, rear (92mm for now unless 120mm fits) as exhaust, riser feeding the GPU, nothing else because nothing else fits. The Cablester cables are already ordered for Classic. I'll post simultaneous CPU + GPU load temps once it's built.