you have like 3 elements: the mesh, the rig, and the animation.
the player model consists out of the mesh and the rig and is one file.
each animation is a separate file - so you basically shouldnt try to export more animations to one file. I am not sure if this is a requirement from RE, or just for more comfortable replacing of single animations, but I wouldnt stray away from that style.
And about iqm - it does work for me, it is just not perfectly documented.. you have checkboxes for mesh and rig there, and a text field where you can enter the name of the animation(=action) you wanna export.
So it depends a bit on what you wanna do - if you just want to replace the player model, then dont touch the animations at all, just select the mesh and the rig, and export these (check de-rigify). You have all animations as single iqm's still in the folder, and it will use these.
That was not really an answer to your question, but hopefully it helps a bit
