You are correct.
The p0data2.bin contains both datas of the enemies (AF) and textures of the battle scenes (Fraggoso's NPC mod).
You can't use AF without the datas of the enemies; there won't be obvious bugs for some time (except that enemies are not changed from vanilla) but it would eventually crash on some key fights.
2 solutions:
• Just use the p0data2.bin of AF and play with non-upscaled battle scene textures,
• Merge the two p0data2.bin. You can do that using just the "Unity Assets Viewer" tool that is included in
Hades Workshop:
1) Install the p0data2.bin of Fragosso's NPC mod (the other files are irrelevant during the whole merging),
2) Open the Unity Assets Viewer (in HW's "tools") and open the game with it (selecting the FF9_Launcher.exe),
3) Open the archive p0data2 inside the UAV and sort the files by their type,
4) In the UAV's options, make sure that the "Automatically convert images" is deactivated ("Don't convert"), it makes things go better,
5) Select all the files of type "Texture2D", right-click and "Export selection"; that's the files upscaled by Fragosso,
6) Verify that a folder "HadesWorkshopAssets" has been created in FF9's folder, containing all the exported files (you shouldn't be able to see the images as they are not converted),
7) Close everything, install the p0data2.bin of the AF mod, reopen the UAV, reopen the game with it, reopen the p0data2, sort the files by type,
8) Select all the files of type "Texture2D" again, right-click and "Import selection". It should print a success message.
Once that's done, you have a p0data2.bin that contains both Fragosso's HD battle scenes and AF's enemy modifications.
I didn't do it myself because, as you said, that makes huge files to upload and I didn't want to multiply the versions "AF + Fragosso's HD backgrounds" / "AF + Fragosso's HD backgrounds + Fragosso's NPC" / "AF + Fragosso's NPC"...