For pepolar fieldmaps, the reference is actually the mean image estimated by TOPUP. In the future, I would like to select as the reference the EPI image that matches the polarity of the BOLD/SBREF file to be corrected, but this works well enough most of the time.
Yes.
Yes. A bad registration of a fieldmap to a BOLD volume would mean performing a warp where the expected signal sources and targets do not correspond to the right locations in the input image. You should be able to see evidence of this in the first two plots for a functional image, in fMRIPrep 23.2, at least.
You really should look at all of it. First, you want to look at the fieldmap report to see that the blue/red distortion blobs show up in reasonable places relative to the brain. (If this isn’t something you have experience with yet, they should at least be ~left/right symmetric in AP images, and focused near the frontal and temporal poles.) Then you want to look at the fieldmap reference-to-BOLD reference registration. It would also be good to look at the fieldmap correction before/after; if you’re not using precisely applicable BOLD inputs, you would expect a little bit of suboptimal correction but you shouldn’t see induced distortion. The coregistration report should clearly line up, though there will be sections where dropout and distortion do not fully recover anatomical fidelity in the BOLD image.
If you want to do things in native EPI space and for that to be a single space within each session, then the sbref hack makes sense (and use --output-space bold). If you’re going to be comparing across sessions, you can use the hack, but I would use fake sbrefs from both sessions to find a space that’s equidistant from both sessions; that way you aren’t inducing more resampling artifacts in one than the other. It’s probably simplest just to target the T1w space, though.
The effect should be pretty small.