Am I correct in thinking that armatures only really work properly in plan view? (zy plane)
As this is the rest position and alt-R (clear rotation) resets it to this. Pressing the ‘n’ key confirms this and shows that absolute global cordinates are used.
At least maybe it is required for paste flipped to work properly? Experimenting…
For flipped poses to work your model should be facing you
(and right side up) when you press numpad_1. Make sure your
armature is facing that way and press ctrl_A (apply size/rot).
Then parent the mesh to the armature. If flipped poses still
don’t work you may need to monkey around with the
“roll” values for the individual bones in edit mode.