Normally, bonus units will give you the bonus points right after a level, such as in the Arena. However, the Tempest Trials force you to do up to 7 fights in a row with up to 4 different teams. I spent the entirety of today raising a level 1 4☆ Nowi into a level 40 5☆ unit to try and reap the 40% bonus since she's a current bonus ally.
The team she was on (Team 1) lost on map 4 of 5 and I was ultimately unable to win on map 5. However, I noticed that I was given more points than a loss should have awarded me. Does the bonus ally simply need to be on any team to get the bonus for all maps or does the bonus only apply to maps that that unit was present on?