Well, I've been running it for awhile without issue. I think the relatively low CFM rating of the Vortech V-9 probably helps keep me safer than I would be with a bigger unit.
I've thought about putting a good rising rate (I have the stock FPR now) just for the added, although probably slight, safety margin. I hate to try and fix something that isn't broke though.
I think with the setup I have now with the water / meth injection probably helps a little also. The Meth does actually add a bit of usable fuel to the mix and the water helps raise the octane of it all.
The MAFTPro can control timing on vehicles / engines with one igniter. MAY be possible to do it with the 1uz's dual igniter setup but I have not pursued the issue with TurboBob (the maker of the MAFT). So to answer your question, my timing is completely stock and controlled by the stock ECU.