In case of monorepo where there are several independent deployment units, separating it via dir is quite simple solution. Additionally, if you move the code to some other provider, you move it together with the code (what is not guaranteed with e.g. GH issues).

However, I don't say NO. It all depends on context, if you decide to use issues - go ahead. I am a fan of pragmatism - do what you need in your context, don't blindly follow the rules