I just recently started using flexible components so your question was of interest to me.
The assembly I am currently working on has several sets of different flexible components in it (all sets of 2).
I have one pair of FCs that are each independently controlled by a measure in the skeleton. They will normally be the same value.
I created a repeat region on my assembly drawing bom. Both FCs show up in a single row, qty = 2.
I then set one part of the set to a different fixed value, so it was in a different state than the other.
They still showed as a single row in my bom, with qty = 2. The attributes highlighted in my repeat region are "no duplicates / flat / Bln by part / No cbl info".
So, it seems to be working as expected for me. Geometry differences in the instances of the FCs don't seem to factor in to the repeat region.
It appears that the FC's can work in the assembly boms as you would expect.
Is there any chance you have any difference in any of the parameters displayed in your repeat region, between the two instances of your FCs?
That would cause separate rows to be created in the repeat region.
By the way I'm on Wildfire 3.0, M110
Hope this helps, good luck to you.