Unfortunately, it seems that marker order creation is the only thing that determines marker layering on the map - none of the setMarker* scripting commands seem to "refresh" the marker to the topmost layer, it needs to be re-created.
Therefore, make the Add custom placed buildings to the map organically.sqf script re-create original map markers after placing down the per-building markers.
It should be fairly straightforward and it seems somebody else has already done something similar:
https://forums.bohemia.net/forums/topic/215656-marker-on-top-of-other-marker/?do=findComment&comment=3401398