Can I get the fmriprep output also in a [91,109,91,200] format?
You can probably reset the bounding box with nilearn or some other tool, but fMRIPrep does not directly offer expanding the bounding box.
I’m going to interpret this question in the spirit of “I want to make voxel-to-voxel comparisons between two preprocessing pipelines.” For that, I think even resetting the bounding box would be insufficient, as there’s no guarantee that your voxels are actually aligned. You’re better off performing a rigid registration with AFNI’s 3dvolreg, antsRegistration, FreeSurfer’s mri_coreg, FSL FLIRT or SPM’s coreg. This should handle both alignment and resampling, at which point you will have results as close as possible to comparability. You could also try something like mri_robust_register to output to a halfway space, to ensure that both images are equally distorted by the registration.
An alternative is to perform voxel-wise comparisons in the template MNI space, and then perform some summary statistics of interest in the T1w space, to explore further.
Is the fact that there is no skull-stripping in the final fmriprep BOLD output an error? Is there a way I can obtain a skull-stripped output BOLD file from fmriprep?
That is the case, and yes, you can apply the brain mask found next to the BOLD series.