Reproduce:

1. fresh 1.4.3. install
2. install Making History (without it everything seems to be ok)
3. install Kopernicus and Sigma Dimensions 0.10.1
4. set 6.4 resize and rescale (without rescale everything seems to be ok).
5. create new vessel with engine shroud.

https://imgur.com/g7HaNaL

SD does not affect vessels so I don't really know what could be going on there

I'll look int it

can you try using some clamps to keep the vessel elevated?

Yeah, I tried with clamps:
https://imgur.com/16cGJNo
I also tried using struts and Kerbal Joint Reinf - no changes. As I said, it is fresh install, just 1.4.3+MH+SG.
Game Data Folder:
https://imgur.com/qnGeMpG

I'll look into it, but I have no idea where to start from since my mod never does anything to parts / vessels

can you send me the craft file you are using?

@Wuzetek this is a stock issue. I have confirmed this myself. It is definitely exaggerated by rescaling the bodies, but the issue is not with SD

Here are images from a completely stock game:
HERE, HERE and HERE

The fix will need to come from Squad. I just made a bug report on the official tracker.
https://bugs.kerbalspaceprogram.com/issues/18862

You can go upvote that issue want Squad to really pay attention to it.

@Galileo88 nice find, thank you!

Oh, thank you!