have you tried fluke? works for me, tags and all, no conversion needed.
sure, encode and tag the flacs on linux, import them directly into itunes via fluke. or maybe I'm just not understanding what you want to do.edit: just to be crystal clear: fluke lets you import flac files into itunes. they are not converted to another format, but they play back within itunes and itunes can see the tags.
one more thing, it sounds like you are getting into distribution... note that pretty much everyone who is selling/distributing lossless is using flac and they usually have a faq somewhere that walks users through getting itunes and wmp to work. this has been going on for years so users must be getting it. at that point you also have a chance to move some of them to better software; there are lost of programs on mac and windows that support flac natively and do everything itunes does including ipod sync.you can peruse some of the online stores for their verbiage about getting itunes and wmp to work.
I can rip a track to wav using cdparanoia then convert it to WAV -> FLAC -> Apple lossless -> FLAC -> WAV and it still has the same md5sum.
the ffmpeg alac encoding<->decoding should match, the question is whether itunes can always decode it. alac is proprietary, ffmpeg's reverse-engineered encoder may not be compliant, it may not always decode in itunes, apple can change the codec at any time and things break with a new version of itunes, etc. that's the risk you take.