Mnišovský's report

[ReneZ]

But is it a viable hypothesis that Rudolf II actually bought the VMS for 600 ducats thinking it was a Bacon original?

What he bought for 600 ducats (florins, really) was a set of manuscripts, the Voynich MS being one of them. Who exactly believed that it was a Bacon original is not clear (at least to me) and in any case Rudolf may have relied on advisors. 

There is of course a remaining chance that Mnisowsky was mistaken about which MS was/were acquired for this sum, but we have no argument that supports that. (He was there, we were not...).
More details on Voynich MS day.

However, I seem to recall Voynich writing to someone in Europe asking for him to find information about Jacobus.  If that is correct, was that before or after he saw the signature?  

For the details, see here:
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Jacobus is a big name among the Jesuits.  He was one of only a handful of "notable people" in the court of Rudolf mentioned by Schmidl, on par with Ticho Brahe.  If Voynich had consulted sources like Schmidl while looking for suitable Rudolf->Baresch intermediaries, he would have stumbled on him, and would immediately have known of his fame as a herbalist and his role as Rudolf's personal doctor.

Schmidl was a Jesuit writing a Jesuit history, and Tepenec (who was not a Jesuit but still a catholic) was treated in detail because he left the Jesuits a fortune in his testament. With respect to the court of Rudolf, Tepenec was one of many hundreds of barely significant 'extras'. He was never Rudolf's physician.
Voynich only consulted a historical novel, while his aide Herbert Garland found out who was Tepenec from more reliable sources, for which see the above link.