ArcGIS Pro 3.2.1:
There's a new toggle in geoprocessing tools that lets us choose to use the highlighted/selected records (toggle enabled) or all records (toggle disabled).

Disabling that toggle means the tool will ignore filters on the layer (definition query, time filter, range filter [and a selection layer's "selection definition set"]).
I would like to have the option of ignoring the selection, but honoring filters (like a definition query). I have standard definition queries that I apply to almost all FCs/tables, such as STATUS=ACTIVE. It wouldn't make sense to ignore those definition queries in GP tools just because I have a selection.
The enhanced functionality could look something like this: If the selection toggle is disabled, then provide an option to honor filters: yes/no.
Related: Original Idea - "The input has a selection." - slap a clear button in there!