Actually, scratch that. I see now the game is still running fast, no matter what. I have suggested myself by the fact that it actually is still quite playable and some minigames (hospital, top down ants) look normal. The rest, I thought maybe it's down to my NTSC TV. But after comparing it with a cycle-exact version on my PC it's definitely a bit faster.

So I've spent the whole evening yesterday trying to sort it out, to no avail. I've also remembered discussions about this subject here over a year ago: https://retropie.org.uk/forum/post/105234
Basically it boils down to RPi's Amiga emus lacking the cycle exact option. Some games require it, especially in WHDLoad versions. Barbarian is another good example. The "solution" was to run adfs of these games instead, but for ICFTD it does not work either. Bummer.