Hi Ofir,
I've expirienced more then once developing hebrew websites using eZpublish CMS.
I'm afraid your question is irrelevant since RTL issue is related to the templates you create and not to the translations engine.
Since you are creating a siteaccess for each language you will have a different design folder for each lang. there you could easily design a RTL template and a LTR template separatly.
I hope I'm answering your question. Feel free to ask.
Lior
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