I think I've figured it out.
So, my theory is that the phased reload animation ID calls in the game are hard coded. Meaning, if you add an extra animation before the phased animations, then the ID of the phased animations will change and the game won't be able to find the said animations (hence why you get the default T-pose).
So, in order for this to work the phased animations have to have the same ID as they do in NW. Meaning, no new animations should be added before
["reload_musket_full", 0, amf_priority_reload|amf_use_weapon_speed|amf_play,
Furthermore, you don't have to use crossbows_as_firearms flag in the module.ini for this to work. You can give the weapons which you want to use phased reload the itcf_reload_musket flag, and this will turn on the phased reload. With this, you can have 2 reloads for your firearms. One phased, and one non-phased (which can be different than the phased one).
I think I'll have the muskets use the phased animations, and make a new non-phased animation for rifles and carbines.
@deadknight
I'll send you my reload sound file via PM. The timing is off though. You'll have to time the reload in game then match the various sounds of the reload soundtrack by editing the sound file. I think reloading a musket takes 15s, the sound file is only 12s long though.