There is only one action which does something like that now, which is the new "Swap Tiles" action in the context menu of the tileset view when having exactly 2 tiles selected. Though of course, that replaces all tiles A with tile B and all tiles B with tile A. The action is available in the development snapshots.
What I could imagine is to add an option to the "Select Same Tile" and the "Bucket Fill" tools for ignoring the flipping flags. Though at the moment there isn't a good place in the UI for adding this. It could also be a more global toggle like the "Random Mode" button.