So, what the ACA is supposed to do? When setting in the menu PAL mode in theory you are forcing Agnus working in PAL mode.
Correct - that's what the option does. However, software that runs later than the menu may override the setting, as I explained before.
Or do I have to isolate pin #41 anyway?
This will be the safe, but inconvenient option. YOu might want to explore the WHDload option first, as that does not involve removing the chip and possibly putting the computer in danger (no offense - I just don't know what level of experience you have).