My dumped retail disc games are larger and missing the patches/DLC.

[Uzuki]

I'm trying to make my own FPKGs for Ni no Kuni 2 and Valkyria Chronicles 4, but the app dumpers I've tried aren't seeing the patches or DLC. Rather, it can see the 4.00 patch for Ni no Kuni 2 but not my DLC for it, and for Valkyria Chronicles 4, it seems the 1.01 patch was merged with the base game but my DLC is missing. On top of that, these games are 30GB in size normally, but when dumped they're over 50GB. Why is that? What am I missing?