Thanks for the patch, can you submit it here? Makes it easier to review:
Can you move rna_armature_apply_transform into an ED_ function and let it share code with ED_armature_apply_transform?
DAG_id_tag_update does not need the OB_RECALC_DATA flag in this case, it's only for Objects, instead use 0.
This patch breaks compilation of blenderplayer, you need to add a few stubs in source/blenderplayer/bad_level_call_stubs/stubs.c (same as e.g. ED_mesh_transform has).