@AmigaMance,
I haven't tried mos on pup for a long time (and even longer since i used 3.9), and i can't remember how frogger behaved, but maybe the additional 68k was welcome in that case, even though context switches cripple that kind of parallelism. You could also try to use wos/pup version of frogger, in case mos version had some issue.
BTW, i also can't check on powerup hardware right now, and results will probably differ, but i just checked a 320x240 mpeg file with both frogger and mplayer, and guess what, frogger eats 25% CPU while MPlayer eats 16% on my pegasos2 G4 (probably more recent libavcodec, a bit more optimized).
In any case, as you said, ambient and mui are irrelevant, as they just idle 99.9% of the time when unused.
About Ambient, the fact that it uses MUI adds some slight overhead. However, workbench is certainly NOT much faster. As a quick test, just try and display 1000 files in ambient and workbench, in icon and list mode, and see who wins. In any case, Ambient just does a lot more than Workbench, and everything comes at a price. And if you really really prefer Workbench, you can still use it on morphos instead of Ambient. Compatibility is a good thing sometimes.

Menus can also be made non-transparent by editing skin config, but from what i remember it was not really slower than magicmenu on os3.x.