Well PPC executables are larger than 68k ones. New kernel, memory system, Intuition, new icon format, larger resolutions, backdrop images, etc etc....all take up more memory.
The Blizzard PPC can take up to 256MB of physical ram - the Cyberstorm PPC 128MB, and with additional memory via disk-paging or zorro 3 memory boards, I don't see it as a problem.
If I run OS 3.9 on a high colour screen using a graphics card I'm also never going to be able to run it in 2MB.
You can't compare it with a stock OS 3.9 install with no graphics card.
We are pushing the limits of the Classic architecture for sure - trying to get the most we can out of it while providing the latest version of the Operating system and providing some extra fun for Classic PPC users and the capability to run all the AmigaOS 4.1 applications.
If you want to run a pure classic system using only 2MB of ram there are other alternatives like a Minmig or stock A1200, CD32, etc.