The right-click menu in the reference tool shows "vector object actions" which is already confusing, but if you have a selection on your raster layer and select cut in the menu, not the currently selected reference image is deleted, but the selected pixels.
I can confirm this for the Apr 04 5.0.0-prealpha (git 4e05187) appimage. The Transform options do work on the refence image. Setting to Confirmed. (If it's been Assigned, does it need to be Confirmed?)
The menu name and cut ,copy and paste are implemented in this MR https://invent.kde.org/graphics/krita/-/merge_requests/798 . They still don't work with the global shortcuts (e.g Ctrl+C) because Reference Image Tool is not connected to KisSelectedShapeProxy . As suggested by Dmitry KisSelectedShapesProxy can proxy only one source, which is usually a shape layer. That is, if you have a vector layer active and activated a reference tool, then the layer should be temporary deactivated as shape selection source.
Closing since the MR was merged.