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I know little about the python part of pyrosetta.
In the underlying c++, the function src/protocols/loops/loops_main.cc::set_single_loop_fold_tree does not appear to modify the input pose in any fashion other than replacing its FoldTree object.
FoldTree does have an == operator in C++; maybe you can use that to check if your FoldTree and the function’s are identical?
Conceptually and upon a casual reading of the code, I can think of litte that set_single_loop_fold_tree should be doing that cannot be straightforwardly replicated by manually setting up edges (and I’ve written a LOT of code to do manual loop edges). The only thing that comes to mind is re-rooting the fold tree…perhaps it changes the root and you do not? The rooting function is called reorder (although the root is still called root.)