You don't say if you have designed and built SMPS's or converters before.
If not, you are going to have a steep learning curve, since you are talking about a >1kWatt system. Selection of the controller is the least of your problems, PCB layout, EMC, power switching component selection, heat sinking, power inductors, and capacitors all present as important, if not more important issues.
Simulation using LTspice (and design with PowerSim, which gives values, and shows you how to wind inductors) help a little, but the simulation component models are not often adequate for anything other than an initial trial, in the end you have to put it down on a PCB.
Your specifications, 0-40V out for 12-48 in is very broad, duty cycle limitations preclude many/most solutions, boost/buck, ZETA, or SEPIC are not used for these power levels (they all have the ability to have an output voltage above and below the input voltages). It would help if you could relax some of the specifications, do you really need them to be as broad as they are. Your first decision has to be the circuit topology, from there you can start looking at a design.
I would personally avoid a micro in the control system, the code has to be bullet proof, which it rarely is, and you have to use best practice in dealing with code going off into the weeds, watchdogs etc.
You need to get good advice from someone on the forum who has designed high power SMPS's to get a clearer perspective than I can give you, all my work has been
