When using bonded channels in 5GHz (40MHz or 80MHz bandwidth), Mist RRM uses the lower channel of the bond as the primary. (ex, if bonding channels 44 and 48, it will select 44 as the primary channel).
When manually running the RRM process via Network>Radio Management, the “Optimize Now” button only triggers the RRM process for the band that is currently displayed. If you want to optimize both 2.4GHz and 5GHz, you need to switch to displaying the 2.4GHz Band, click “Optimize Now”, then switch to the 5GHz Band, and click “Optimize Now” again.