It's a tech issue.
I have confirmed, that if we remove the level gating on the shell item, the mods will still affect HK (Even though they are level gated), making him a super companion for low levels. We would likely need new tech to fix this issue so the mods level takes precedence over the items level. While I'd like to get to this tech someday, it's pretty low priority compared to the other things that I (and most of you guys) want.
I'd love it if the fixed tech was mods or gear that auto-leveled with the player. This is something a lot of people want for other items as well so making the tech for HK it could also have other uses too. Just a thought