No, the system board original data is preserved, unless your messing with specific detailed areas of the bios image.
Mainly the ME FW/region is the only not touched during the flash, unless the update is instructed to do so if has lower FW version or requires it.
This is how it works using original ASUS CAP files or mods.
My question was based on the most used method to flash mods on Asus board supporting this feature, advisable here in the forum flashing guide (Asus boards Section), still valid among most of modern Asus boards/chipsets, with USB BFB feature.
What you did with the FPT tool, is the correct option, preserving an original system backup with valid system board data.
This data can be viewed/transferred in a emergency/recover, using a simple useful tool called FD44 Editor
“modified bios like completely…” user undefined goals…
Hope it helps you, good luck and enjoy the forum.