PKHaX interaction with ROM hacks?

[NopeInserts]

Recently I've been playing around with editing Pokémon base stats through tools like DSPRE. However, I've been running into a slight issue; I've been having an issue where when I edit a Pokémon using PKHaX/PKHeX and place it back, it reverts the base stats to the values before the DSPRE edits, is there a way to circumvent this or am I stuck with this? Is there a way to edit the base stats PKHeX works with? Or will I simply have to be patient and grind out EVs and friendship?   

[Kaphotics]

PKHeX does not support ROM Hacks. Stats are calculated using the personal info data from the unedited game.

PKHeX automatically calculates stats unless you click the checkbox to define stats yourself. 

Stats are not saved when stored in box, and stats are recalculated when you heal them in game.