In general, a property tag alone won't indicate a prototype. Remember: Apple is a large-ish corporate entity that itself needs tools to do its work. It's not unreasonable to think they might use one of their own products, when it exists, to do that work.
Most likely, if you find an item that has an Apple property tag on it, it was "purchased" by Apple to do some kind of work.
Whether that work was administrative, manual-writing, graphic design, PR, accounting, programming, or whatever, there won't really be a way to tell.
Property tags can be a neat addition to a system though. I have a PowerBook 180 with a Princeton University property tag, an SGI machine with an NIH/Behesda property tag, and a few other things tagged for the local university.