What's the problem of it being canon? It's not like the story is ruining the game.

But it might in the long run.
For starters, the comics have their own mandates which sort of contradict the games. Dr. Eggman being the only known human in the comics, everyone else are animal people. Even Central City which was a human-populated place in Dreamcast-era games, is all animal-people now.
However, TailsTube and Shadow Generations reaffirm the world is still shared with humans.
Another concern of mine is, if the IDW comics are the same canon as the game, anything that will happen in the comics will be reflected in the game. Let's say, hypothetically, IDW Sonic comics goes through what Archie Sonic did with Penders, where Pender's forced the comics into a corner and had to restart their own continuity.
**Imaging** if Ian Flynn was the one who pulls a Penders on Sega and IDW. Not only would that mean the characters he made for the comics will have to be pulled out, but SXSG, Frontiers and all games starring Tangle and Whisper might also be blacklisted over it.
While it's highly unlikely Ian Flynn will pull a Penders, especially given Sega and IDW likely have procedures and measures to prevent after what happened to Archie Sonic, if anything bad happened
in the IDW Sonic comics, it will be reflected on main continuity.
Here's another "What if", let's say IDW Sonic comic gets a new writer/artist who introduces a new friend for Cream the Rabbit who gives off creepy-vibes but seems friendly and not too out of the ordinary for Creams friend-group. And a few years later the writer/artist turns out to be a kiddy-fiddler! Sega and IDW can fire him and never use his characters again, but given IDW Sonic comic is "canon" to the games means the character exist in Sonic's continuity.
I know I'm being super-hypothetical, but i believe Sega claiming IDW Sonic comics being canon to the games is a red flag to me.