I've not really had any issues. I do try to line them up and I typically quicksave before adding anything to a base or really any complex structure, but that's not a Pylon thing, that's a "can't sleep, Kraken will eat me" thing. I did load the game back up to start on Phase 2 (Kethane infrastructure, all built on-site) and ran into a problem. I built a new launch pad (intending to keep it as a spare, as the one I had was having trouble staying upright) and from that moment on, any time I loaded the quicksave both pads would explode. First one, then the other. I played with it for quite a while before giving up and flying in a new pad, this time a Launchpad 2 just for something different. Here's what the base looks like now (from the opposite angle because sunrise): Left to right across the image, we have the deployed LaunchPad 2 connected to a Pylon with a pipe (this seems to keep the pad from jumping around.) That pylon is connected to another slated to be the home of the Kethane infrastructure. Next pylon is connected to the Workshop-that-looks-like-a-HOME-habitat on one side, and a small smelter on the other; the smelter is in turn connected to a large ore canister with two ore drills on it. (Two for balance, no other reason.) Last pylon has the original metal delivery container on one side, and three large Parts canisters on the other. The first Parts canister was flown in, the other two built on-site; the third one in the row as a large Recycler on the front. The command ship is attached at the end. The pad, metal bin, first parts container, and command ship are the only items flown in from Kerbin. The Workshop, second Parts canister, Smelter, and Ore mining vehicle were all built from the metal in the delivered container, which pretty much emptied it. All the vehicles are mobile, though the pad is only through flight and the metal bin is nearly impossible to drive. Everything else including the workshop uses legs for stability and rover wheels for transport.
