Sort of. You can't limit labels to a project, they're global for the field and don't care what project they're used in.
But, you can add a new field of the type "label" and limit it to one project (or a set) - that makes it independent of the global labels.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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