Is it possible to duplicate a tile within a tileset and then make a flipped version, and then also make another duplicate and rotate it? So for example there could be 3 alternative versions of the same tile. This would mean that instead of having to rotate or flip a tile after it had been placed on the map, the already flipped or rotated version could be added directly from the tileset.
Also, is it possible to export to a text file (e.g CSV) that just contains the order of the tiles by layer, for example:
Tiled does not edit images, so if you want to edit your tileset image to add additional tiles, even if they are just rotations, you’d have to do so in an image editor.
If your game engine supports flipping tiles though, I recommend using Tiled’s flipping instead of adding dedicated tiles, since it allows your tileset to be smaller and easier to modify. If you need pre-flipped tiles as a convenience, consider making a map to use as a sort of palette, where you store common arrangements of tiles and copy+paste from. (Neither of these solves the problem of Tiled’s terrain tool not supporting flipped tiles, but I believe that’s being worked on.)
Although CSV is not one of the default export formats, you can create your own export format via script. Documentation here.
If you only need this a few times and don’t want to write a custom export format, you could save your map as a TMX with CSV as the data format, and copy+paste the CSV data from the TMX.