I'm using mostly the "flip glitch" and the "duplicate glitch" to merge ship parts without collision issues. You can check out the techniques on this older build video of me: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-AI_1RfN0aWY.html But I think searching for a guide video with better explanation on youtube how to do these glitches could be easier to understand.
@crazy-tommy I got it now. I am a fairly experienced ship builder myself, but I didn't know linking 2 parts together could allow something to shift lower than it would normally. I think I am going to give it a go now! Thank you.