Hi @Seraph
The tool itself needs this same reference data available pre-processed in order to include certain data points in the output. Galaxy isn’t doing anything extra, like building the complete index, for the complications you describe. Even if the index-building functions for Bioconductor tools were also wrapped, the inputs would all still need to “match up” for those features/identifiers.
To be clear: the tools available in Galaxy are the same tools available anywhere else. The “galaxy part” just adds in some extra bits around the original tool to make it nicer to use in a web interface that supports workflows, other tools written by other developers, and throughput features. The original tool itself is still always sourced from the same general tool packages (usually the conda version).
So, I don’t think this is a “bug”, instead, this is just how it works with limited reference data.
You could follow up by reaching out to the Bioconductor authors. The small slice of extra data you need might be something they could layer into the “limited reference data” functions (that part isn’t Galaxy specific either, and part of the underlying tool).
Not a great answer but I am not sure how to help more!