I have found some ways to lessen that problem a lot. First of all use landing legs (the bigger the better, those included with Karbonite work like a charm and they look awesome) in everything you build to get clear of the landing pads when the vessel spawns. Sideways drones have that issue because the core probe is closer to the ground, but it is not unique to them. Another thing you should do is when you get out of time warp when the building is done, wait until everything is completely settled after physics are engaged, because even if a single part is moving the probe might clip and it goes poof.