That doesn't make it a reboot. Prequels rarely do line up perfectly. ADF's Humanx Commonwealth prequels don't. The SW prequel trilogy doesn't. And that's ok, too.. . . it will never line up perfectly with TOS and that's okay.
Then again, TOS doesn't line up perfectly with itself, either. And if that weren't ok, then why was there a TAS, that actually took the material seriously? Why were there TOS movies? Why was there a TNG? A DS9? A VOY? An ENT, a DSC, a PIC, an LD, a PRO, or a SNW?
For that matter (and if you're a Fundamentalist, and this offends you, TOUGH!) The Bible doesn't line up perfectly with itself. Which is something that becomes very clear if you cover-to-cover it as a Lenten discipline.