@meequz if you want a different feature that behaves in a different way to custom-commands certainly make a feature request as @codebrainz suggests.
IIUC one of the Geany contributors has a prototype of an addition that supports all the combinations, run command and insert the output, run a command with input from the buffer but don't paste the output, and the current behaviour. An issue that requests the right thing may elevate completing that in his personal priorities list.
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