I presume you mean to add constraints in Modeller when using the Rosetta-generated model as a template. But isn’t it possible to generate constraint files (i.e. NMR-like constrains) for the rest of the structure (excluding the disordered loop) from the homology models and use them in Rosetta? Are you aware of any script or program that can generate constraint files from a .pdb file?
In this way the ab initio structures will be more consistent with the homology models. Moreover the packing of the regions where the alignment is good may have an impact on the conformation of the loop, and since Modeller tends to be more reliable in prediction of evolutionary conserved regions, the ab inition predictions will be more accurate. Does this make sense?