Just a quick follow-up – I ended up using omni to generate an undistorted EPI, which I then fed into fMRIPrep. Since omni normally outputs undistorted images in template space, I applied the warpfield myself, following a similar procedure as here. However, since I performed the unwarping on the motion-corrected image, I first had to undo the motion correction before replacing the raw EPI in the twin-BIDS directory when running fMRIPrep. I also updated the corresponding JSON files to reflect the header changes.