The problem seems to be solved by using an earlier version of QSIPrep (tested with v0.10.0 on Singularity and v0.12.2 on Dockers).
After changing the version, another error was found with the BIDS conversion, which may be particular to the dataset, and was addressed by manually changing the “TotalReadoutTime” in the JSON files based on this earlier post: Stuck when run QSIprep on HCP data. This modification did not work with the latest version of QSIPrep.