I’m not sure on my terminology, so please set me straight. I have WoW Legion installed on lutris. I would like to install a few supporting applications in the same, I think it’s called, prefix. These apps update mods and mod data. I would love to install the twitch desktop, but I’m not sure if it will actually run in a prefix or not. Help?
To run a program in the same wine prefix:
Right Click on the game->Run EXE inside wine prefix
As for the twitch desktop application, winehq says it wont run so sorry 
https://appdb.winehq.org/objectManager.php?sClass=version&iId=35642
Im using a no-frills python script which updates my addons without any unwanted spying or data collection: Lcurse
Lcurse is not installed into the wine prefix, it runs natively on any linux system. You can put it anywhere in your user home. Note that you need to install the mentioned dependencies and additionally the package python3-cryptography.