Ordering a cert for wildcard and root together requires two DNS challenges

I use Route53 too. In the console you just add additional record values in the same record. See pic below.

In the api I think you just add separate values for the record. I use the api but not for TXT like that.

This pic is a partial from a very large acme-challenge test record

That's probably fine. Route53 usually syncs its name servers in less than a minute. I think there is an API call to check if a change has sync'd. Which is probably best.