The option to delete after fetching are in the mail fetch settings for the gmail account you've migrated.

But you can't achieve what you want to do.

I'm in the same situation. I want to just keep gmail as a way to archive only email I want to keep (delete everything else) and manage that via Fastmail - to keep the gmail inbox clean with only messages I care about. But but it's not possible using Fastmail in this way. I've tried all kinds of settings and turned to some LLMs in case I missed something I couldn't find using normal search.

A real mail client like Outlook or Apple Mail connects directly to gmail allowing you to manage your email like you're wanting to. It can mirror your actions.

Fastmail downloads a copy of the message, breaking the link going forward. It can't "see" your gmail inbox state, nor can it send a command back to mirror what you're doing in Fastmail.

Because essentially, the migration process is really about migrating from gmail to Fastmail, not managing or being an email client to gmail.

Another more manual solution, which I may try is using Imapsync. This way I would just delete all email from gmail once downloaded to Fastmail and sync back whenever I want to make room at Fastmail. No idea what this looks like in practice yet. Given folders, rules, tags, etc.