I don't know the exact performance impacts, but it's basically a trade off of memory usage vs computation time.
If you flip the tiles on the x/y axis you are adding computation time because the gpu/cpu has to perform the flip operation at runtime, but you reduce memory size because tileset image is smaller.
If you don't flip them and just create extra tiles in the image then you are adding to memory because the image is bigger, but reducing computation time since there's no flip operation to do at runtime.
So it's really up to you and your goals. If your game runs at 60fps when flipping the tiles then it might be better to save on memory.