Add
zoom=auto
to your config. It's fine for most games. It was default in FS-UAE 2.x which was a better choice IMHO. Perhaps it comes back in 4.x
If "auto" looks wrong somehow you can use
zoom=640x400
for NTSC like resolution games and 640x512 for PAL 4:3
You can also switch this at runtime with Meta+z. Which is Meta+y in reality on a german keyboard. A bug, I never reported, hehe.
Because I use
keyboard_key_f11 = action_zoom
as a global default anyway... Was a default setting in 2.x as well.
Oh, I forgot to mention: don't use pimped Amiga 4000 configs for games that where designed for Amiga 500 unless you want to enter the world of guru. :-) You games will not run faster/better.