Yeah, I don't see it mentioned much but Colors represents a reboot of the series, putting us in the post-modern Sonic era. It marks the beginning of simpler self-contained plots by the (then new) writers pontac and graff, with all of the characters' development rolled back (Sonic no longer takes anything seriously, Tails is useless, etc).
With a little retooling, this comic would've made a perfect game to change up the status quo and open the door for so many interesting plots. Would Gerald and Maria work with GUN to appose Eggman? Would they try to redeem him? If nothing else, it would be cool having them give Shadow advice during missions and develop gadgets for him.
You're definitely right about their refusal to reference things in a meaningful way. Even Generations references that didn't affect the plot, even Heroes' plot directly tied in to the previous games (Metal Sonic's rivalry with Sonic, stealing froggy to obtain Chaos' data, Team Dark's entire plot).