hmm i dont quite follow... are you able to provide steps?
I'm able to extract the DLC .nca file into a folder, but how do i merge with the game?
Actually you extract the romfs folder for the base game and the update first as a folder, then you extract the dlc which is section0 cause as you said there will be mismatch if you attemp them together. See these commands for instance:
1. Merge base & update as folder: hactool.exe -k keys.dat --titlekey= --basenca=Splatoon2stock.nca --section1dir=romfs --exefsdir=exefs Splatoon2Update.nca
2. You'll get an exefs folder and a romfs folder. Then you use this command for the dlc: hactool.exe -k keys.dat --titlekey= --section0dir=romfs --exefsdir=exefs Splatoon2dlc.nca