hmm, that is honestly the first time i've heard of a worksytle like that. especially with github which is designed to allow for incremental updates to repos. oh well whatever works i guess.
just note that it will likely only be convenient to you and not to others who might want to follow the project.
also, sorry but i'm still a bit confused, what exactly do you need a fork of cc65 for? AFAIK you usually fork projects to modify their source code, but in this case you just want a custom target for it. so why not just download the pre-compiled binaries and follow their official tutorial?
https://cc65.github.io/doc/customizing.htmli did the same with my own 65c02 SBC, i got a folder for cc65 programs that also contains a config folder with the crt0.s file, C standard library, and the .cfg file for my hardware. all according to that page.