Methods for varying insert size in E. coli clones
Yes.  In principle you will have a vastly increased ability to customize the boundaries of each protein domain with a primer and PCR based approach.  It is not obvious to me that the Gateway Cloning System is required, or necessarily the best choice for this approach, but that is likely subjective.

Are you familiar with, or aware of, the efforts of the SGC (Structural Genomics Consortium)?  My understanding (now somewhat outdated) is that they were going to design/use a semi-automated way of implementing the strategy you discuss (domain trimming) so that they could us a high-throughput approach to define crystallization conditions for their targets.  Perhaps you could adapt their method(s) to your protein of interest?