Editing transliteration should be a simple affair. After all, it only uses a few alphabetic signs. Alas, it isn't.In the original MdC, a simple, ASCII-based standard was used. But this standard requires special fonts, where "a" are not "a" but "ayin". This lead to many problem when texts where exchanged. Passing from Mac to PC was a real problem, and publishers were very unhappy. Hundreds of hours of unnecessary work was spent converting files - or re-typing them.
Normally, Unicode should solve all those problems1. So, currently, JSesh proposes choices to the user. Your personal choice will depend on what you want to do with your texts. It's quite likely that unicode is needed for most publications, for instance.
You can choose the way transliteration will be dealt with from the Preferences menu.
as I have written elsewhere, I feel that Unicode for Hieroglyphs is a whole different business. ↩