Yes, but the final boldref is currently calculated from the corrected time series. So I guess it had to be aligned, as I think about it.
According to @jsein’s post ([mcflirt related behavour] FMRIPREP: Strange motion estimations in confounds_timeseries.tsv (lots of zeros)), MCFLIRT under-estimates motion when aligning BOLD to sbref if the contrasts are sufficiently different. So it’s not inducing motion so much as failing to correct for motion.