Partial roof repair: what material to use...?

Having worked in the RV industry for decades I have seen way too many failed Eternabond applications to ever recommend it in the manner noted. When I run into a problem area around a skylite etc. that just doesn't want to seal, I take the entire vent or skylight up and start over as having removed it the underlying problem normally becomes apparent.

I think it is very difficult to do a patch job on a roof and end up with it looking like anything other than a patch job. You can patch in a rubber roof with rubber, but you will always see it, although it may well be completely water tight.