It would be unlikely to have any specials that I was unsure of which primary mag they were a part of. I would either know, or I would have no idea they were part of a primary mag at all. With a large enough cover scan I can confirm a mag's parentage, but since the Japanese Internet is designed primarily to be mobile/bandwidth friendly, it's unusual to find anything larger than thumbnail size, which makes reading the fine print impossible.
It's also perhaps a bit unfair to think of things in "primary mag" and "secondary mag" order. I use the term "special edition" since that's what the direct translation is of these things, but the way they're marketed and sold to the public is as completely separate titles. This is why any reference to the parent mag is usually so small and unnoticeable, since they aren't trying to convey that it has any connections to the parent mag. I tried to touch upon my thoughts on why this is in my original post - I believe it to mostly be a case of politics between the publisher and the newsstands to insure that new publishing ventures get a chance to prove their worth before leaping headfirst into launching new titles.
And how does one decide what is primary and what is secondary? If I were to sort things in the order you describe, Dengeki PlayStation Vol.1-4 would be listed with the Dengeki PC Engine issues, and the first issue in the Dengeki PlayStation database would be volume 5. That doesn't seem right to me, since Dengeki PlayStation Vol.1-4, despite having been published as special editions of Dengeki PC Engine, have nothing to do with Dengeki PC Engine, aside from the word Dengeki, which just about every mag from that publisher shares. They were clearly released with the intent of launching a new, completely unrelated magazine. Perhaps there's a lot of red tape or expensive legal fees when officially establishing a new publication title, so publishers are hesitant to do so until they have a proven success?
Let's say the Sports Illustrated swimsuit issue was published on a monthly basis, and from front-to-back was nothing but pictures of girls in bikinis. Now let's say that the Sports Illustrated logo was nowhere to be found anywhere on the cover, and instead the logo on the mag, and what it is universally known as, is Girls in Bikinis. Remember, there's no such thing as a subscription, so no one is going to get one of these in the mail just because they subscribed to Sports Illustrated. No, they can only be found at the newsstand, where to all but the most attentive eye, the mag is simply called Girls in Bikinis. Why would anyone who didn't see the tiny print in the corner of the cover linking it to Sports Illustrated have any inkling that the two were related? They wouldn't, which is the publisher's intent. It's being marketed as a completely separate mag for all intents and purposes.
I suppose the opinion of which is primary and which is secondary might depend upon which ones were successful enough to be turned into separate mags, but setting up a system based on exceptions just proves how overly complicated this is.