Finally solved my problems, here is how i've done it :
1- Once you have extracted NCAs of the base game, decrypt the larger nca using this command (illegal stuff hidden of course) :
hactool.exe --titlekey=BASE_GAME_TITLEKEY --plaintext="Decrypted.nca" BIGGEST_BASE_FILE.nca
2- Then use the decrypted base nca file and encrypted patch nca files to generate updated RomFS.bin :
hactool.exe --titlekey=UPDATE_TITLEKEY --basenca=Decrypted.nca --exefsdir=exeFS --section1=RomFS.bin BIGGEST_UPDATE_FILE.nca
3- Extract your newly generated and updated RomFS.bin :
hactool.exe --titlekey=UPDATE_TITLEKEY -t romfs --outdir=romfs RomFS.bin
EDIT :
Here is what I archieved so far, Unlocking all items and editing their price work but it had some issues, for example the game freeze when I try to fight offline with Kefla. I tried many mods, most of them make the game freeze after the loding char screen (for example custom hairs)...
I didn't try to progress through story but I assume it will probably freeze too. Modding this game with 1.10 updates seems very unstable...
EDIT 2 : Finally found a way to edit super souls!!! Now my lv4 char is now as powerfull as Goku Mastered Ultra Instinct, including auto-dodge