The CR90 that has the rule where overlap does not effect it, does this also apply to collisions with other ships? If it does apply in collisions also, does this mean the other ship does not take any damages also?

It states only for obstacles

Lyraeus has it right.

It would cause some very weird gameplay issues if they let it avoid ship collision rules.

Clearly, Jaina's Light has Hoban Washburne at the helm, he can thread a needle with that bird. This allows the Light to successfully navigate asteroid fields, and debris fields - but overlapping a ship is just smacking right into it, so there isn't like flying into the ship, but also navigating successfully around it, if you take my meaning.

Thanks and makes sense. I was wondering about the ship overlapping as a second thought, thinking maybe its because the ship is more nimble due to size and modifications. but than again, as wide open as space is, if you collide in space you deserve to take all the damage you get.