If the power and endurance of maneuvering thrusters is being reduced overall, how will some of the larger ships that don't have VTOLs be able to take off and land without burning them out?

If they don't have VTOL mode, they can't take off, is pretty much the answer.

There is a line that can be crossed where things become a one-way trip. Yeah, there's no way around it. Again, this comes back to what I said before: just because they don't look like they have big VTOL thrusters doesn't mean they don't have them. But things like the Javelin, if that decides to go in atmosphere, that's going down, as people have seen on Daymar, and that's not coming back up again.