Yeah, I also thought about it. Maybe even better post an issue at Executor 2000 which is an actively maintained fork.
From further playing about I now suspect that Executor simply fails to load the proper palette somehow. For example, after the Blizzard logo (also in the wrong pal) you first see the title screen like this briefly before it gets the normal palette. The same happens on win/lose tally screens. Also if during gameplay you select "About Warcraft" from the menu and then close the info window, the screen will be briefly rendered in the correct palette. It appears that loading the proper palette takes some time, at least in Executor, during which some errors occur for some reason. I'm hopeful that this can be remedied more or less easily.
The observed behaviour is clearly an emulation bug that cannot be remedied by tweaking setup settings (FYI the Mac version does not have an external setup utility, everything is set in-game). I have already tried out most if not all options provided by Executor for configuring how an app should be running (including some of the command line options), although I do not deny that I might have missed something.
UPD: I just watched a video of how the game runs in a proper emulator and I'm almost certain that the palette glitches occur when the game is supposed to do fade-in or fade-out animations of the screen.