You may want to talk with the Professional Off-Shore Fishermen. They are using a lot of Outboard powered Center Consoles. (Granted, you are looking at a Bennington pontoon boat) However, the point is, those Off-Shore guys expect durability, performance, fuel economy and best bang for the buck.
It is my understanding, the Off-Shore guy expects a minimum of 12 to 1500 hours out of their Yamaha 350's. They run those engines hard. Subject to failure, it is also much easier to exchange the outboard engine. The decision would typically compare initial cost, warranty period, Technician expertise, cost of operation, performance and residual value.
Further, the I/O lower unit has a fixed "X" dimension. Wherever the lower unit was initially installed is where it remains. The problem with that includes skag to road surface, Prop shaft height for CG change and performance adjustment. The rebuttal may include "Just trim the out-drive out to address those points". However, "dialing in an "X" dimension out-drive" can be somewhat frustrating. The Pontoon boat has a long deck allowing the load to move about. That moving load then moves the center of gravity sweet spot out side of the desired "Envelope".
While not a perfect world solution, IMHO, the Yamaha 350/Hydraulic Jack Plate combination is the best choice.