Basically, because there are two basic ways I can see where someone can become "invisible", in the sense that they could gain an advantage in combat.
- People are physically unable to see you. You can be optically transparent, have a psychic shroud, fire a gun through a portal in a separate room, or have some object blocking line of sight.
- People are unable to see you as an enemy. The household servant, the face in the crowd, the wallflower at the party, the bum passed out in the alley, the squirrel in the tree, etc.
The rules dance around the ability to "somehow see" an Invisible person, in such a way that it's clear they're not restricting it to only a single method, such as the See Invisible spell. Therefore it should not be uncommon to be able to see an Invisible target.
The rules for hiding do not say you lose the Invisible condition when you are "seen", but when you are "found". As long as an enemy does not recognize you as an enemy, you remain "invisible" to them.
The rules for using a Disguise Kit in 2024 are vague at best, from what I've been able to gather. In 2014, it explicitly allowed you to change your appearance, and use your proficiency bonus on the roll to do so if you had proficiency in the kit. But we also know that there were movements to shift from making skill checks with toolkits directly, and instead use standard skills in conjunction with the toolkits, such as Sleight of Hand for lockpicking.
So it seems to me that that clearly fits the same sort of conditions to Hide: Be out of sight of an enemy, and make a Stealth check. If you slip into a side room and use a Stealth check with a Disguise Kit, that seems to lead to exactly the same mechanical benefits as you'd get for staying out of sight, for as long as you are not "found".
In this case, being found out would be someone seeing through the disguise — making a Perception check that beats your Stealth check. Otherwise, "These aren't the droids you're looking for."