Hmmm, you are right in that purchasing a stat gain roll for all your stats using Background options does not have a clear moment to be applied in ERA.
During level up, you get the dialog to roll for gains on all your stats.
When purchasing a TP, you get a dialog to roll for the stats that are affected.
While sending DPs, you can click the button to be charged 8 DP for each gain.
So, if you need additional, free of charge, pre-level up gains obtained by spending a BO during creation, there is no way to do it automatically.
You'd need to roll outside of ERA and manually change the temporaries before leveling up.
You could use the Stat Gain option to help you determine the new values, then cancel the level up and edit the stats manually.