I took some time today and created a mod to remedy this problem, called "Shapeshifting Origin Tags" (no idea what else to call it, haha). Basically I made it so origins tags are preserved when shapeshifting, and you can now talk to companions while they're shapeshifted. Reflection and party decision dialog should work for them too now, though I haven't tested that personally.
Links:
Steam WorkshopNexus
