Within the filter, you can allow participants to be added to the Program once every 90 days but that wouldn't prevent a new contact on the account from getting an email mid-quarter.
To solve this, we could have just run a new Program every end of quarter but instead I build one Program to run continuously using a query and included a couple transformation tasks to find the Last Day of the Quarter based off an Opportunity record's Close Date.
Then another transformation task to filter only if the Last Day of the Quarter equals Rule Date. Thus, the Program syncs on the last day of the month but only on the last day of the quarter are Participants added into the Program.
