Yes I guess the reduced Z travel could be a limitation for some kinds of projects. You also have to add on how far up the macro retracts the spindle after probing, on top of the thickness of the plate itself: none of that Z travel is usable for cutting, though it is true in general that retract height isn't usable for cutting.
I suppose understanding the Z limitations imposed by the probing process is worthwhile, including whether the software lets you fine tune things when it gets tight.
It helps a lot though that you can raise and lower the spindle in the mount on Shapeoko, so (at least for me) it would most likely only come into play when doing really deep cuts (I think). That's been my own experience using a touch plate so far, at any rate: that is, it hasn't really been an issue on the XXL because in practice I can't really use the full three plus inches of travel for the kinds of projects I do on that machine. But I can see how some heavily '3D' projects might be constrained.