Sorry, I should have clarified that I have not yet tested the latest version of the hangar. My last career in KSP (with hangar, of course) was... 3-4 months ago. Also my craft files (if I could find one) would be riddled with parts from various mods. So definitely not a clean reproduction of a bug.
I suspect (but this is just my uneducated guess) that when the game loads in a ship with... considerable partcount inside a ship with... more parts, some lag occurs and the ships end up clipping briedly even when it should not mathematically happen.
Other problem is that some of my ships do not hold constant heading, but instead wobble around a bit. Unbalanced reaction wheels or something. So soon after when the ship from hangar spawns, the mothership turns a bit and clips into the ship. Of course, this is fixed by just turning of SAS. Can't say that this is a fault of your mod.
I remember trying to use VTOL hangar(?) in space, but I think it required the ship to be landed? The asteroid gateway might work for me quite well. I had not tested it, since I thought it requires an actual asteroid to function:)