Is it normal to keep seeing the `.fly.dev` domain name (even though I have a custom domain)?

E.g.:

Checking DNS configuration for index-flow.fly.dev

Visit your newly deployed app at https://index-flow.fly.dev/

This is now wrong because I’ve assigned a custom domain.
Is this a configuration issue with some part of the config not yet set for my actual domain (indexflow.io)?

Or, is this just poor messaging on the part of the deploy script?

Yes that’s normal. Fly isn’t a DNS provider so it only knows about the guaranteed <app>.fly.dev domain. Your DNS and Fly are 2 separate entities, so I wouldn’t conflate the two… that’s to say the messaging isn’t poor nor incorrect.