Regardless, "slight" touch-downs were considered 2-footed, flawed and were not credited under 6.0; that's not really debatable. Thus, Maria's lutz and flip would not have been considered completed triple jumps.
Underrotations, OTOH, weren't as cut and dry, as evidenced by all the discussion here and by the wide range of marks for Lu and similar instances, like many of Bonaly's free skates. The most likely scenario is that anything less than 1/2 turn cheat was considered a minor mistake, but that the jump was still counted albeit with less credit, similar to a hand down. Lu was probably given credit for all but the final triple toe (and triple flip), with maybe a few judges considering one of the lutzes as being lower quality. The toe, sal and loop were all fine under 6.0 - and I think the lutzes were, as well.