Email in Queue, SpamAssasin error

If I set emails to be sent via the Queue, and allow a small number of emails to be sent every time the cron job runs, I run the risk of SpamAssassin marking my email with the “DATE_IN_PAST_03_06” flag (for example).

If I understand this correctly, this is because Mautic “creates” the email, puts it in the spool folder and then sends it later, and ofc if I “spool” 1,000,000 emails and only allow for sending one per minute, they will be old.

Am I right in the assumption (that it works this way)?

The process is essentially the way you described.

You can set a flag in your swift mail send cron to send a specific number of emails per trigger and then set the cron to trigger at a time interval as little as once per minute. It will take some math to get the interval correct but it is possible with the right hardware and php/db tuning to accomplish your goal.