First the writers get shit for making the tech on DIS too advanced in the first two seasons. Now they get shit for not making the tech advanced enough! Those poor people just can't win no matter what they do!
Anyway, we know from VOY that faster-than-warp tech (let's just call it all "transwarp") exists, but that doesn't mean that even the 28th Century Federation had the resources to deploy them on a large scale -- or that if they did, that they wouldn't be vulnerable to the Burn as well. It's possible, for instance, that coaxial warp drive, spatial folding transporters, or Borg transwarp coils might still require matter/anti-matter reactions regulated by dilithium to power their components. And we know from "That Hope Is You, Part I" that quantum slipstreams are within the technical capacity of 32nd Century ships, but that the benamite required is extremely rare. So it's plausible that the loss of most dilithium would still have the effects described, even if Starfleet and the UFP had transwarp technologies by the 28th Century.