Mark,
The answer is yes.
The CT 36 AutoClean is the exact same machine as the CT 36 from the standpoint of its filtration system. You can purchase the HEPA filter separately and install it and it will function just like a CT 36. As you suggested, I would highly recommend that you disable the autoclean function while using a HEPA filter so that the filter is not compromised.
The CT 36 AutoClean is not designed or tested for use in RRP applications. If you need an extractor for RRP, I would suggest one of our other dust extractors, which have been specifically tested for that application.
Shane