I think the reason for the inconsistency in reliability is cause of the two types of engine.
So far, personal experience and empirical evidence from the forum shows quite clearly that the A3 engine/trans is very reliable, and the A5 (A35) engine/trans is not.
Part of that may be due to the very poor IDM brand CDI Units many early Targas were equipped with, so if you do go with an A5 (A35) system, make damn sure you're using Bosch or Iskra CDI unit, or you'll prolly be sorry in short order, cause it's about $200-$250 to replace one of those damn IDM's due to parts incompatibility.
Was it me, I'd hedge my bets, and go with an A3, but possibly consider putting the A5 head on it (and yes, it will fit) for greater heat dissipation.
Both are 38mm bore x 43mm stroke, and the ports all match up fine....my original consideration on this thought was that the A3 cylinder running full-out for a long time on a hot summer day would begin to overheat, which is a receipe for disaster, over a period of time.