But wouldn't Snively's presence be a problem for them?
Depends. When would take place in the timeline? How much of a threat was Snively? What would have ol "Red Eyes" done? Since the third season never happened we don't actually know how much of an effect Snively would have had on Mobius. And even if he was, would he be defeated during the Adventure arc? There's not good answer for this question so I've been function on the belief that Adventure would be Season 4ish and Season 3 would be over at this point in time.
My take was that had SatAM been revived to coincide with SA1's release as was originally intended, Hurst might've used the opportunity to continue the story where it left off. Thus Snively would've been the reigning villain like in the show's ending.
The red-eyed anomaly is still a mystery, though. Hurst might've claimed it was Naugus, but I can't help but be a little speculative about that. Not only do the eyes resemble that of Sonic's rather than Naugus', but the whole mystery ending seems unnecessary since we've already been introduced to Naugus earlier in the series. Had the cliffhanger been resolved, it wouldn't have been much of a surprise reveal if Naugus was the character behind Snively all along.
If it did turn out to be Naugus, I could picture him telling Snively about Chaos' imprisonment within the Master Emerald and how to release him. Who knows? Maybe Naugus was the enemy the ancient Echidnas were battling long ago and that he survived into the "modern-day" to finish what he started.
Had the show gone on to adapt SA2 as well, I can imagine the space colony ARK tieing directly into Hurst's original plans for Robotnik originating from a space station.
Who knows? Maybe the ARK was the reason why the animals of Earth survived and evolved into the Mobians, and project Shadow was the indirect ancestor to Sonic. But that's a whole other can of worms.
Maybe to soon to open that can of worms but...
You could use Ark, or the battle of Ark as the excuse why there are no more Humans. Maybe Robotnik and Snively are the only survivors?
Another great idea. After all, there has to be a reason why it's called the "ARK".