I believe the recommended pipeline would be to use the optimally-combined output from fMRIPrep, which, if you requested standard-space outputs, should be in a standard space.
That way, you don’t have to transform anything.
I can’t speak to the within-network and between-network connectivity measures, sorry. I might maintain a resting-state functional connectivity workflow, but I typically use task data to validate denoising methods. Maybe @dowdlelt could weigh in on your findings? Assuming you’re not covering the same topic in Compare two protocols for TEDANA.