Certbot might not do this out of the box but ACME lets you pass one challenge at a time, collect a new one, repeat. The tokens which show you passed a challenge will "keep" for at least hours and it might even be days (when Let's Encrypt was new it was weeks!) so you can collect them up to get your cert over a time period.
So, as long as the challenge taking is serialised you can get away with just giving a single TXT answer at a time.