adding a layer "by hand" with CD_DEFAULT (initializes data correctly to -1) seems to do the trick, not sure though if this should/could be handled in a more generic way?

In D5003#114191, @Brecht Van Lommel (brecht) wrote:

I think there is a deeper issue here, booleans should not have to do anything specifically for facemaps.

BM_mesh_bm_from_me seems to be using CD_CALLOC, using CD_DEFAULT instead may help?

That was my first intuition as well, but that "fails" as well. Digging deeper into CustomData_bmesh_merge (think I am close...)

Some findings:

• in CustomData_bmesh_merge, CustomData_merge is called [in which customData_add_layer__internal would take care of layer creation/data init nicely if CD_DEFAULT is used], but we are calling it with totelem=0
• (this is just for detecting if a change to customdata would take place at all...)
• dont see another place where CD_DEFAULT would kick in
• then CustomData_bmesh_copy_data copies data of existing layers into the (merged) customdata-layout [this initializes with 0 and then copies stuff over], so no call to LayerTypeInfo->set_default()...

So instead of the previous solution, I have added code to CustomData_bmesh_copy_data that would take care of setting to default, will post in a bit...
This seems to work nicely (e.g. also vertex colors are now initialized to white)

note: it might be good to pass an option to CustomData_bmesh_copy_data to controll whether this is done or not (since this called from multiple places)