Given that the 2.0L and 2.3L engines are the same block, ie: identical outward dimensions, there's nothing preventing anybody from installing a 2.3L in a MX-5...apart from coolant-line re-routing and minor other issues typical of a FWD transverse layout to RWD longitudinal layout swap.
All of the previous Miata engines were also in FWD transverse use throughout the lineup, and the current engine is no different.
In regards to IC location, for the MX-5, it would most certainly have to be in-front as opposed to on-top...similar to the 2004-05 Mazdaspeed MX-5s and all aftermarket turbo (and some supercharger) kits for the 1990-2005 Miatas. There are already a few companies developing supercharger kits for the 2006-07 MX-5, and one working on a turbo, that I'm aware of.