I'm not sure MLB really views the taxi squad as a COVID-emergency roster, just a replacement minor league roster, with enough bodies to be able to credibly have workouts and simulated games. Even if there is some kind of COVID IL, I don't think it is going to apply to the 40-man roster, so very few of those players (except relief pitchers) will ever sniff a major league game, and no more than 2 or 3 at a time. And if it does apply to the 40, and teams actually get to where they are using players 50-60, there's not gonna be a season, as much for financial reasons as safety reasons.
Certainly the contending teams will do it differently than the ones who aren't contending.
In theory teams should just be able to keep their unready prospects around without them being on the squad, but I guess they need to limit the number of players who are allowed to be anywhere near the field (whether it's CBP, the practice field or Allentown), and won't have enough coaches.
I assume they are allowed to have more than 60 players for spring training, assuming proper precautions (different workout times as well as the multiple locations)? Because if not they've already got cuts to make, and it would be impossible to invite this year's draft class.