SmartEX tickets and transit within Tokyo - how to avoid IC card issues?
On my last trip, I ran into an annoying issue - I traveled from Shimbashi to Shinagawa planning to buy our shinkansen tickets at Shinagawa (seemed like the easiest way to just get on the next shinkansen without missing it or waiting around). Instead, I got really confused in the transfer area - these machines only let us buy one ticket at a time because they require exactly one IC card to operate, and they wouldn't even read my wife's apple wallet IC card.
For future travel, I'm trying to find the most foolproof way to do this, and it seems like that's using SmartEX (which we ended up doing last trip too) or, for JR East, Ekinet. SmartEX tickets are station-to-station, so it removes all the confusing "travel within Tokyo is free but only if you use JR trains" and "a shinkansen ticket is actually two separate base fare and limited express tickets" stuff, too (I'll happily pay a couple hundred extra yen to keep things simple).
So let's say I have a SmartEX shinkansen ticket attached to my IC card, and I'm starting at Shimbashi. I tap my IC card in and travel to Shinagawa. Can I use the shinkansen transfer gates with my SmartEX QR code? Or would this mess up my IC card and I need to exit the ticketed area and re-enter through the main shinkansen gates?
And is the answer the same if the line I took to get to Shinagawa are not operate by JR? Say, the Asakusa line from Asakusa Station? Is there even a way to transfer to the shinkansen from these Tokyo Metro lines or will I necessarily leave the ticketed area anyway?
Lastly, is this any different for tickets purchased and added to my IC card through Ekinet? I've never used it but may in the future for a JR East shinkansen.
Thanks for your help!