I don't think there is any roster to "submit" on the 31st, whatever your 25 was on that day no longer matters practically. If you're on the 40 or the 60-day DL before September 1 you are in the mix, and if you have any guys on the 60-day they can be replaced by any of those other players (it is still position-specific, yes). The bigger injury exception is when you petition to use someone who wasn't even on the 40 before 9/1 (as was the case with Brandon Finnegan). So let's say the Phillies call up Cole Irvin on September 10 and he turns out to be lights-out in relief. If Eickhoff is still on the 60-day DL they could try to make him playoff-eligible.
I'm all for being conservative with Ramos's injury but if he thinks he is going to be ready in a week or two they probably aren't going to be able to talk him into a falsely extended rehab, nor is there any reason to considering Knapp has options.
As for the future, who knows what Ramos will be looking for. But he's probably in decline (his defense might be better than what we have but it's also not what it once was, understandable given the last injury). The nature of the position leaves a lot of options though, especially if he only merits a two-year deal. Three years, he'd have to understand that he's probably the back-up by halfway through it.
The Nats might still come after him. Of course they are also really interested in Realmuto so if that's the case, our taking Ramos off the table doesn't make the Nats worse (except on the farm).