I think the answer is "eventually". My reasoning is that Ford will prove their point one way or the other at Le Mans in 2016 and for a few years after that, and after Ford exits will do just as they did with the GT40 when they turned the stock over to Wyer and others besides Ganassi will run them (provided the prove competitive). But they'll want to keep the privateer competition down until they get their company branded run at it.
The truly race prepped cars will have quite a high price tag associated with them. Since the cars are produced under contract by Multimatic they could be allowed by license to build a few extras. Who knows. Multimatic is pretty good at what they do and may even have "continuation" plans in place after Ford's 4 year production run (assuming 1000 units @ 250/year = 4 years). In fact, as I think about it, the platform has legs and maybe going beyond the 4 year run like this is how they recoup some of their tooling costs.