Assuming that I use the BAM for showing compliance with the minimum energy performance prerequisite do I have to use the BAM also at the simulation for EAc1?

It would be more meaningful to use the values of table 9.6.1 (space-by-space) instead of the same LPD for every space types in the building. However the ASHRAE UsersManual states on page G-36
>>If the building area method is used, it must be used throughout the whole project.