Just get rid of the shroom drive, and bam. fixed.Fact: the producers continue to urge fans to be patient, that 1) apparent canon contradictions will be explained; and 2) we will end up with the "optimistic Trek" of TOS.
For both of these to happen, it would have involve significant change over the remaining 9 episodes. In fact I don't see how you can get there without something like multiple universes, time travel etc. Including the MU involves a significant change and an alternate unuverse, especially if we are talking multiple MU episodes. It's seems reasonable that the MU would play an important role in the story, not just a couple of side episodes.
Or maybe my thinking is completely off.
Or the producers are lying.
Not that hard.
We're still 10 years away from TOS, they have plenty of time.