I haven't tried to play FreeSpace on an Amiga yet, but wouldn't any of the expansion packs work with the Amiga conversion of the FreeSpace game engine?
In principle yes.
Usually with such games that have been ported to the Amiga, only the game engine is ported and all the data for the game is used "As-Is" with no alterations of the game images, sounds, music, etc.
Some total conversions (specificaly ones involving FS2) Are geared toward certain versions of the FS2_Open engine and don't like it when you try to run them on others. I have read that some straight up missions can be a little tricky if they've been written for engine versions later than what you have.