Do you have TSLRCM from the Steam workshop? If so, then yes, the Steam workshop works completely different compared to TSLPatcher. I suggest you read this guide.
Basically: The Steam workshop will create new folders where it simply dumps the workshop mod content and when launching the game will take all these files and if a file is present in two locations it will choose one based on some kind of priority list. There's absolutely NO merging when it comes to .2da, .gff or even .tlk files.