I have wrote a MultiQC module for seqfu stats that was recently merged (MultiQC/MultiQC#3271) and is part of the MultiQC v1.31 release (https://github.com/MultiQC/MultiQC/releases/tag/v1.31). This module should provide some nicer plots and sample name handling for the reports that is not possible when supplying it as "custom content" as we do currently.
The nf-core MultiQC module have no yet been updated to 1.31, but there is a raised issue here: nf-core/modules#9014.