If you have multiple repos, you can't have an atomic commit between them. Pretty much period. I'm scared to hear what you mean on that.
Ideally, all tooling makes the separate nature of the projects transparent. They should test separately. They should deploy separately. If that is not the case, then yes, they should be in the same repo.
I've worked at places where they would "solve" this problem by letting the build break while all the commit in various repositories land all at once. It's really bad.
Ideally, all tooling makes the separate nature of the projects transparent. They should test separately. They should deploy separately. If that is not the case, then yes, they should be in the same repo.