Setup didn't migrate much from Time Machine. Should I run Migration Assistant now? I set up a new MacBook Air, asking it to migrate everything (or nearly everything) from a Time Machine backup on SSD of a 5-year old MacBook Air (both on Mojave).

After configuring lots of settings, I noticed that Migration Assistant didn't copy in user settings, documents, or applications after all. It did get the user name from Time Machine.

Q. Is it a good idea to run Migration Assistant now to overwrite the user account? Is Migration Assistant likely to work after silently failing the first time?

I assume it will copy in settings like WiFi credentials and discard the work of fresh settings including Touch ID.

See: How to move your content to a new Mac.
I followed the recommendation from an Apple Support chat to run Migration Assistant. It succeeded in migrating the user account, apps, and docs.

I let it replace the user account that I had started setting up.

It required some follow-up steps like enabling the extensions for the anti-virus software and the network backup software.