Do we know that backprop is disjoint from variational free energy minimisation? Or could it be that one is an approximation to or special case of the other? I Ctrl-F'd "backprop" and found nothing, so I think they aren't compared in the paper, but maybe this is common knowledge in the field.

Yeah: and people have made comparisons (which I can't find right now). Free energy minimisation works better for some ML tasks (better fit on less data, with less overfitting) but is computationally-expensive to simulate in digital software. (Quite cheap in a physical model, though: I might recall, or might have made up, that you can build such a system with water.)