Combining .xml files will not make any difference, because what is likely slowing down the sim is not the number of xml files, but the path the add to the sim to search the add-on files so, if the sim is slower to load because it have, let's say, 30 new paths to search file into in 15 xml files, it's unlikely it will load any faster if it had the same 30 paths in a single .xml file.
Not that I tried, but I think this is what it happening.
No, there's no way to load sceneries in any other way, if we add a path, it's because we need it and, in fact, our way of adding paths is already very efficient because, for example, all our sceneries that require Simobjects will take them from only two paths ( Misc or PBR ), regardless how many sceneries you have. All our sceneries share a single path for Scripts, and all our product share a single path for the software modules so, it's difficult to be any more efficient than that.