Keep in mind this could be some internal thing that doesn't relate to what we know about the games. If you are posting about your games, make sure to be clear what region they are from.
So I checked all of my games and only found the tags on 6 of them: (A) in BTG and both versions of Dive Alert and (B) in Shanghai Mini, Puyo Puyo and Pac-man.
The tag is present in both the cart and the front cover. All are clamshell releases from 1999, with the A ones having consecutive serial numbers and Shanghai and Puyo Puyo too.
Would be interesting if other forum members could check these to see if all have the same tag or there are different versions of those releases.
I didn't realize the serial numbers were close on many of these, good observation. It could be a coincidence, but it could be relevant. I don't have any of these japanese releases, but I searched online for versions differing from what you found and I could not find any without the circles.
That's an interesting thread. I only have NTM and Pac-Man and both have the aforementioned letters. However, my Pac-Man has the letter only on the cart, not on the insert.
My first intuition was it might has something to do with first hand and third party developers. But that's a rather thin theory as Dive Alert was made by Sacnoth (which however was owned by SNK). So A would be games developed by SNK and B by 3rd parties.
Another idea that came to mind could be the use of periphals. B for cross-rings and A for the wireless communication (???). But I think NTM doesn't support it. So yeah, barrel burst.
Finally how about different regions in one region. Just with PAL-A and PAL-B on the Nintendo Entertainment System. What I mean: there are several variants of inserts/manuals for the games. Then again I have a 3-manual Pac-Man (English/German/Italian) with an English-only insert. And I think Shanghai Mini didn't have a multiple region release, did it?
I'm pretty sure this was something Japan did and it just leaked over to Europe using the same game art templates that were localized. That would explain why later English snapcase releases of Puyo Pop and Pac-Man don't have them anymore. Shanghai Mini only had one English snapcase artwork style that I have seen.
I like the cross ring and wireless idea, but they also featured wireless on the cover, so why use another mark unless it was to match the smaller space on the cart label?
Another random thought I had: if I remember correctly, Pac-Man and Shanghai Mini are two of the few games that don't have save features. But I think Puyo Pop saves high scores, so this doesn't fit either...