Hello Chris,
I don't think this is a "user error". I think Adobe should be able to program a state of the art paint bucket, which is capable to get this done right.
Other applications are able to get this done right.
Please don't fall into a programmer's ignorance ("this is done right by definition") but listen to us artists and improve this unintuitive behavior. Add something like "ignore transparent pixels", because this doesn't even work if you draw on an empty layer.
Thank you!