1) Source? Just because it appeared somewhere doesn't mean it's true. Where'd Sonic Stadium get this info?
As mentioned, it's from a Q&A stream Flynn did over the weekend while playing Lost World. Admittedly, I don't have time right now to sift through the whole thing, so it's second-hand info. Also, the post specified that Robotropolis had never existed at all in the new continuity. Mention of the city not currently existing would not be an issue, as the comics stopped using it quite some time ago.
2) Who says the a retconned backstory is going to be bad? We don't know what the backstory to these characters are, or if it's going to change. You can't say it's "hodgepodge" if you don't even know what they are yet.
This largely boils down to a general lack of confidence in Flynn's writing ability. His poor handling of the Mecha Sally arc had soured my initially positive opinion of him even before all the drama related to Penders kicked in with Endangered Species. If he still had a strong existing framework to build on, Flynn would at least have an easier time writing ongoing stories. Now he has to build an entirely new framework on the fly, one that must provide results similar to those of the old backstory, in addition to dealing with current plotlines. It's a tall order for any writer.
3) The Robotropolis backstory hasn't been much of a driving factor since SatAM. The Comics continuously retcon the events of Sonic's Childhood. First he Met Sally right after Uncle Chuck was Roboticized, then they've been childhood friends. First Sally deems them the Freedom Fighters when they find a hollowed out stump that later becomes Knothole's Main Base of Operations, then it's tribute to a group of never before mentioned Freedom Fighters who started it. First at eight Sonic hadn't officially gone on any missions, next apparently the early issues of the comic were when Sonic was eight. There is no set canon to the group's past other than Robotnik's coup in the first place, which the retcon still can do. In fact, giving each character an individual reason to hate Robotnik would promote much better character development than the "Robotnik just took over" reason.
Once the series got off the ground, it consistently worked with a core premise more or less identical to that of SatAM, even if minor details changed from time to time. While I still am of the opinion that the comics never managed to handle their nuances in such a way as to either capture the feel of the show or offer something equally compelling, that's not the fault of the premise.
As for memory restoration, that's admittedly something that did not occur to me until shortly after my previous post. However, it strikes me as a case of trying to have one's cake and eat it too. If the Robotropolis backstory from timeline A will still be relevant to characterization, why mention specifically that it never happened at all in timeline B? If there's a mandate against its inclusion, not mentioning it at all would be an easy workaround, as readers could still infer that it transpired. Having the characters' memories restored comes across as a means of damage control, one that will likely not have appreciable effects save for a few superficial allusions to Flynn's own work. Sooner or later references to the previous continuity will cease entirely.