I am also confused and very frustrated.
I know it's frustrating but I'll try to walk you through what I did.
This DLC messes up a lot of the hard work MrGT did but there are some workarounds that aren't prefect but can help.
I guess it all depends on what you want.
Here was my workaround that helped me keep all the work MrGT did with the Bundesliga and National teams while still getting updated rosters with one League. (you can choose La Liga, Ligue 1, EPL, etc.) The reason I say one league is because you can only export 20 teams.
So here's my step by step process (assuming you have MrGT's OF)
1. Download the DLC and apply Roster update
2. Choose one league where you want it to be the most accurate (Bundesliga is not an option because with the roster update there were missing players as all teams aren't licensed) ex: I chose EPL
3. Export and save all 20 teams
-Quit Game-
4. Delete Edit File and Data Pack (I'm not sure if they are 2 separate files or if the Data pack is part of the Edit File)
5. Reload and copy MrGT's OF
6. Start up game and you should be prompted to download data pack
7. Download data pack but this time
do not apply roster update
8. Now, import all the 20 teams you previously exported.
Finished product = You now will have the OF that MrGT originally created with correct and adequate Bundelsiga players, correct and adequate National Teams, plus your league of choice corrected transfers. Also, you will see the other new players in the Free Agent Pool where you can manually transfer if need be. If you want to have more accurate transfers for all the leagues, there is probably a different workaround. But what I have done is fairly simple and gets one league done for you efficiently while holding onto MrGT's previous work.