I keep my human readable html rar'ed up, that way I don't really care about how many files the archive contains. If you write the script in a cross platform language (like python) you don't have to worry about portability either. And opf is just a simple XML file. Not really anything to learn and its likely to be around for a while as well.
No you can't specify custom character conversion without editing the source code, but you can embed a font that can handle the special characters into the LRF.
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