1994-95 Distance - Perfectly Understandable
One anti-RS argument I see sometimes is that they weren’t living together during Harry’s fourth school year, and that Sirius was instead flitting around the globe living in caves and such. However, the context of Remus being a recently-outed werewolf and thus under more scrutiny/financial pressure means it would be mutually beneficial NOT to have a convicted mass murderer and Death Eater living with him - I know Sirius could live as Padfoot but he can’t stay like that forever, and the risk would be too high. I bet, Wolfstar aside, that this is Jo’s Watsonian reason for separating them.
To stray into fanon, and depending on how the WW views homosexuality, the scandal might be doubled if they were considered/revealed as lovers. Also to stray into fanon - I know they forgive each other on page seamlessly for suspecting each other, and that’s why we love them, but there might be lingering romantic hurt/awkwardness. Lie Low at Lupin’s happens after a year has passed and when the Order is busy planting false leads (see the Arthur-Kingsley interaction in early OOTP), and they have any protective magic eg wards Dumbledore might cast off-page. Also, Albus is canonically gay so do with that what you will lmao.