Repeating the noun when we referring to it multiple times using different adjectives
Solution 1:
Technical prose has a very different aim to literary prose: technical prose should be as unambiguous as possible. With this in mind, Variation 1 is in my view by far the best. The problem with Variation 3 is that the uninformed reader is left with two alternatives: is a certain kind of type-1 hypervisor known as a native, or as a native hypervisor? I realise that the reader will probably be able to work this out for themselves, but why give them the choice?
And your Variation 2 is just the worst of both worlds.