Wonder if Sega had that much pull way back in the 1990s/early 2000s because it sorta seemed like Archie did whatever (including the Knuckles stuff).
They did, they just didn't care as much and Archie wasn't exercising any quality control. They only got away with killing Robotnik in #50 by promising to bring him back within twenty-five issues (guess who returned in #75), and the issue that slipped in a Sonic OVA reference got them an extremely stern "do this again and we will pull the license"-grade warning in return.
At least, I think it was better that way. It's not completely canon and it's something that could be referenced lightly. With the adaptations being proper issues, it seems it truly is part of the canon instead of a one-off.
It's a more elegant solution than trying to fully adapt and integrate a game in the main series (which they swore off doing after Sonic Adventure for a reason), but you run into a couple of problems, ignoring the logistical ones of producing and distributing extra issues.
The first and probably most damning is that it's just really hard to adapt a video game to a comic. The one-off specials never, ever came close to conveying the full scope of whatever scenario they were based on, and the Death Egg trilogy didn't fare much better. More recently, the Genesis arc and Mega Man game arcs chewed through their material lightning fast, and the source material isn't exactly plot-heavy. You just can't get a satisfying story out of it that accurately reflects the material.
The second problem is that the series has diverged far enough from the game universe that it's terribly awkward trying to make a plot from one directly mesh with the other. SA2, Rush, Rush Adventure, and I think Riders 1 all technically happened in continuity, though trying to figure out how they actually fit into the otherwise fairly tight plotting is nigh-impossible. It's a small miracle that Sega didn't mandate a Shadow or Sonic '06 storyline. Throwing the game plots out entirely and cherrypicking elements from them over time is just a much more organic way to fold them into the series.
So, as intrusive as they are, if they have no choice but to do these promos, the Another time, Another Place method is the least painful way to go about it. They just shouldn't be eating entire issues for the aforementioned reason and because this isn't what I'm buying these series for.
