Yes in MNE-Python the empty room prep function takes care of differences in first_samp to make the empty room data be processed the same way to the extent possible. Basically if you have 3 minutes of empty room data but 10 minutes of task data, you’ll get the first 3 minutes of head positions used to “movement compensate” the empty room data. It’s not perfect but so far seems to work reasonably well for infant data I’ve tested with at least.
It will work incorrectly if the position at the start varies drastically from the position later on, though.