Engineer kit usage issue/bug.
There are a few topics about this; it seems to be a fairly large concern.
As you mentioned, kits do have a base damage, although they do not scale with weapons (and won’t add stacks to any equipped sigil) because when you equip a kit, it unequips your weapon.
Simplest solution would be for Anet to simply have damage, stats, and sigils apply to any kit you swap to.
Yeah this has been an extremely heavily discussed topic since BWE 1. There are more then one topic on it on the front page of the forums here.
See the stickied discussion at the top of the page in bright red marked engineer bugs, for example.
This post was also to present valid points backed by exact numbers, I had not seen other posts presenting it like I did so I thought it would be a good idea to post.
This one is fairly congruent with your discussion, perhaps it will help you.