I'm trying to create a mod with a script that grants a custom perk. I'm aware that the first FormIDs for mod objects correspond to whatever load order you have for said mod. Doesn't this mean that my script using the addperk command will break every time I change the load order of my mods for whatever reason? Is there a way to refer to a mod perk or object in the same esp as the script without regard to the load order FormID?

Yes. You use the name, not the form ID.

The only reason to use the form ID is if you are using the console.