The reason is that the Maelstrom engine is completely different, and as a result, requires different script code (the files found in the Program directory) for all flavors of the COAS, Gentlemen of Fortune mods).
While the Maelstrom engine is capable of playing COAS and GOF, it requires my modified Program script code. I have working copies of COAS and GOF 1.2, 2.0 and 2.1.5 in Maelstrom, to allow playing vanilla COAS and the GOF mods, but I have never released them to the public.
Currently, the only version I have released for Maelstrom is ERAS. If you want to play COAS or GOF with Maelstrom, one has to wait until I release them, which I plan to do in the near future. When this happens, you will also be able to play native 64 bit architecture as well as 32 bit all the way back to Windows XP.