If the member who posted the question is not satisfied with the engines the way they are, take the boat back to your dealer and turn it in.
Buy a boat that you can fully tilt the engines out of the water, this boat is not for you.
After all, how many choices do you have given the situation?
As far as the intakes getting screwed up and causing problems because you can't fully lift them out of the water, then you are not familiar with outboard engine design, or have never seen a boat with an inboard or I/O - and wonder how they get the antifouling inside those long water passes!
No outboard, inboard, or I/O engine manufacturer will ever design such a motor that can't be in the water 100% of the time. There are many who dock in places there is no room to raise the lower unit at all ever, as well as the commercial boats used for dock building, bridge maintenance, etc.
Do you think these guys tilt their engines at the end of the work day, if so, why?