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A large part of MsgEd TE and the underlying message API has been made independent of little/big endian or structure packing issues. This means that in principle you can compile MsgEd TE on Alpha, PowerPC, Sparc, or whatever exotic hardware and it will read and write exactly the same binary format files like the Intel versions do. You do not even have to specify any special compile-time switch for compiling on big endian hardware.
However, some things do not yet work on big on non-Intel machines. This includes:
This means that you presently must restrict yourself to a Squish message base and a squish.cfg configuration file if you want to run MsgEd TE on big endian hardware. This will be definietly fixed in a future release.