The thrust line for a surface piercing propeller is different from ditto for an i/o drive, and the sp drive trim function is NOT for changing the boat running trim. The hull design process for a sp drive is not different per se from the process for any drive, but you have to consider the thrust line variations as a function of speed and load.
That said, erratic behaviour of sp propelled boats can often be traced back to bottom shape or weight distribution that is not suitable for spp, somewhat analog to what happens with waterjet installations. A hull (or center of mass) that is good for i/o drive is not necessarily good for a straight shaft, sp propeller or waterjet.
There are numbers of Arnesons (and Levi drives, Surfury drives aso) successfully operating in commercial environments; the point is: the hull must be adapted to the drive. Both Arneson and the other suppliers will assist in this process, provided they get involved early, but don't expect them to save your bacon if you install their equipment without due knowledge.
As always a reasonable SOR is the starting point; getting in love with a particular hull and creating a well-behaving vessel by "backwards engineering" is seldom a comfortable route. However, a driveline specification, adapted to the SOR may very well be a starting point for a successful design spiral.