It probably depends who initiated the concept.
I can imagine that if Phantasialand approached Vekoma and said "we've got this rough concept, can you help us figure something out", Vekoma might (fairly) ask Phantasialand to cover at least some of the prototyping costs. There'd be some negotiation then about using that ride technology on future rides (for example, an exclusivity clause).
If, on the other hand, Vekoma had some up with the flyer concept entirely themselves, and simply needed something to show off (and to help with development of the hardware), then they probably footed the bill themselves.
The most likely answer is probably some horrible mix of the two with a complicated contract in place. What we can know of for certain is that it's probably a closely guarded highly commercially sensitive agreement that none of us will ever get the pleasure of reading!
In terms of costs - I'd wager you'd get something like the FLY prototype knocked together for under a million. You don't have to worry too much about lots of other things that cost lots of money - complex site works/access, statutory approvals, complex track design/dynamics (both design and manufacture costs), reduced/zero profit margin, in-house labour, etc, etc.
I speak with no experience of building coaster prototypes, though...