When you dump the Nand from GW, you get the WHOLE Nand which consists of Firm0, Firm1 and CTRNand. The FAT16 Xorpad is for the CTRNand only which is why it is smaller than GW Nand Dump.If what you need is only the encryption - just get yourself the FAT16 xorpad to do so.
However since there should be padding and junk difference, you would have to decrypt the GW NAND dump and compare it to.
Once the padding or junk is solved, you could use rxtool dump with xorpad to encrypt it and flash it back.
I've an easier idea, no need for actual hardmod if anyone would like to have a try.
GW Dump (SysNAND), RxTool Dump (SysNAND), EmuNAND Dump (Emunand tool), FAT16 Xorpad (RxTools).
Once you have all those above.
1. Decrypt the GW one and EmuNAND one with Xorpad.
2. Compare decrypted GW one with RxTools one.
3. Once you have offset and solved the padding, get RxTools one encrypted.
4. Backup all files within your SD.
5. Use Emunand Tool to restore the Encrypted RxTools dump to Emunand.
6. See if it works. If yes, the emunand would be same one as your SysNAND.
7. If it works, you could flash the EmuNAND dump back.
To me, the Xorpad has smaller size than GW one. Don't know if it meets the length of RxTools one, yup.
If such a method work, you could tell devs and you may even have a Format EmuNAND option in RxTools.
The Nand is Firm0 + Firm1 + CTRNand.