No, the objection to not keeping .DS_Store per folder and doing it per file system instead was that a non-Mac might make changes that would not be seen. The point is that this can already happen for a lot of different reasons! So keeping it per folder doesn't eliminate the failure mode, it just makes it slightly less common… at the cost of annoying all non-Mac users and any Mac user who needs to interact with Git etc. The tradeoff analysis for doing it per folder is bad.
No, the objection to not keeping .DS_Store per folder and doing it per file system instead was that a non-Mac might make changes that would not be seen. The point is that this can already happen for a lot of different reasons! So keeping it per folder doesn't eliminate the failure mode, it just makes it slightly less common… at the cost of annoying all non-Mac users and any Mac user who needs to interact with Git etc. The tradeoff analysis for doing it per folder is bad.