So I was able to get the Black Emporium and mods working without issues (SO FAR). I had to do a bit of chicanery to do it, though.
When I first attempted to play DAI with mods after merging them with the fresh new ModManager V.50, it CTD - wouldn't even open the game, actually. Figuring I had corrupted files, I removed the mods completely, put my copy of P7 files into the Update folder, and did a full Repair, which took a while.
After that, I put the patched folder in as 'Patch' and did NOT leave the vanilla folder in. I also incremented the version of the package.mft in the modded Patch folder by one. After that, I was able to see my mods, use the Black Emporium and the mirror, and craft, all without issue. However, I didn't get to play a lot.
I think repairing the files might be key before using mods with the BE installed.
One thing I DID note was that the modded hair did NOT show up in the BE CC. However, I only had a female Qunari of the four origins with hair mods who have gotten to Skyhold, so I can't verify with any elves or female humans. Can someone else verify this?