It's difficult to explain, but no matter how many times Kaito shows up, there's the fact that he hasn't been involved with the plot, and that's where importance lies (as weird as it is to say with how scarce the plot is).
The argument of Kid being important and by extension his universe really shouldn't be made unless he was involved with plot. If he's not, which he hasn't, then it boils down to cameo. It's difficult to wrap your head around it, but just imagine it this way: imagine Gosho isn't also the author of Magic Kaito. Then what would Kaito's appearances be?
A cameo.
That's all it is. The high number of appearances? That's because of the convenience that comes with Gosho being the mangaka of both series.
I can't find the specific link right now, but as an example Conan has made a cameo in a manga called Hayate Combat Butler (or something along those lines). He was even referenced by name. In fact, I believe he's had quite a few references in that series. Does it mean he has anything to do with the show? Considering the only thing I know about that series is the few cameos made by Conan and nothing else that could be a summary, I'd say not.
It's the same with Kaito's situation. The reason I found out about Kaito's story was because I looked up
Magic Kaitou. The only reason I found MK was because of a comment on related to his third appearance. Kaito appeared 3 times and among those I learnt
nothing about Magic Kaitou, and I would've continued to be oblivious of his own tale if I only watched DC.
It is my belief that one universe should only equal the other if they're important to one another or explicitly stated to be the same place (ie: certain Tamora Pierce books). If Kid's universe was = to Conan's, we would've known more about him. In essence, the word "universe" here could be thought of as "series".
So, thinking of it that way, Why is Kid in Conan's "series"?
Cameo.
Conan has his own "series" or universe: Detective Conan
Kid has his own "series" or universe: Magic Kaitou
Are they the same? DMeatgeicct iKvaei tCooun a n
If they were, the above should've been either DDeetteeccttiivvee CCoonnaann or MMaaggiicc KKaaiittoouu as I was compariing the spelling. It's not the same, therefore the universes should not be thought of as the same

At least that's the way I see it. Another answer would be what mangaluva said: MST3K mantra
In essence, don't think too much about it
