As to A... I might have to move them, but if the plumbing is in the bottom, I have to REMOVE them all. If it's plumbed through the back, I only have to drain it to the point it's plumbed, and then move the rock from the back, from the area of the plumbing and blamo, I'm there. What worries me is that under the rock a return might get broken or cracked and I'd have to tear everything apart to get to it.
B with the standpipe, I'd have to cut a hole in the top to fit it into whatever overflow box got put inside, or I'd follow Brendan's suggestion (Kudos for that) and build an external overflow box. (Not those stupid CPR types but an actual megaflow style overflow that just happens to have the box on the outside of the tank)
C. The patch could only have a weird failure if the acrylic itself were melted. Weld on basically is a weld... with the holes filled and patched over, unless I were incredibly incompetent and missed the area entirely, there's really no chance of failure. See, the holes aren't just being filled... a patch bigger than the affected area is also being applied. I don't know how familiar you are with weld on applications, but the stuff is pretty incredible. I built my sump for the 58 tank and I've dropped it, moved it with rock in it, had big things land on it (during moving) and the thing's never so much as looked hazed. I'm very confident in my plastic working skills.
Now this doesn't mean I've quit debating... I'm just playing devils advocate here. I want to really look at this from every direction. Personally, I think the location of the holes is awesome, especially if I built a drilled pvc rack into it, with a few loc-line returns around the edges where they could be directed for flow outside the rock, but still concealed by the rock. This tank is going to have roughly 300lbs of rock in it before I'm through, so I really need to consider ease of maintenance. Which is the main reason holes in the bottom make me uneasy. Originally I planned on using them, until talking to some of the people locally where it was almost unanimously suggested that I patch and redrill. I would like to have some soft flow in the rock, and some decent current in the open areas, with a couple returns near surface for surface agitation. I've tossed putting two overflows in, with two surface returns from those, and having the rest of the returns be the pvc rack and loc-line.