That's a really good question, and I'd also to know...
For now, I've read this: http://masteringbahasa.com/verbs-indonesian-formula-examples
Which sort of makes sense to me? Active transitive verb that requires an object. So I suppose the difference between "punya" and "mempunyai" is just formality when you're defining the object in the sentence?
I guess so, though "to have" always requires an object. I wonder whether "punya" sometimes does not have an object, and if so, what that means.
That's great, and I've never seen that site. It sounds from that as if it's simply a matter of formality. The suggestion that there was an infinitive form in classical Malay is interesting too.