The IRONPYTHON.DLL you are looking at is built for AnyCPU.
PE32 from corflags does not mean that the assembly has been built for x86, the choice is between PE32 and PE32+. A combination of PE=PE32 and 32BITREQ=0 means AnyCPU. That is, the same assembly will run in either 32-bit or 64-bit mode.
If the assemblies are bit-neutral (like in the case with IronPython), consider putting them into ~\Shared (eg, C:\Program Files\Manifold\v9.0\Shared or, say, C:\Portable\Manifold-188.8.131.52\Shared), that way Radian / Viewer will see them in both 32-bit and 64-bit mode. You can also use global PATH or put assemblies into the global assembly cache.
If the assemblies for 32-bit and 64-bit *are* different, put the 32-bit modules into ~\Bin and 64-bit modules into ~\Bin64. If you want to use global PATH, it is best to set up different versions of the environment for 23-bit and 64-bit (basically, launch through BAT file). Putting assemblies into the global assembly cache will work, of course, the cache will deal with different versions of the assemblies automatically.