Ok after trying this below I have questions.
So Arashi was incorrect for pointing me there? If so, then I take it tile_get_rotate(tiledata, rotate), tile_set_rotate(tiledata ect rotate), and the like for mirroring, and flipping is code I should use. How does one do that with more than one property at a time on each tile? In the example given in the manual below it only sets one tile's rotation, what if I want to set the entire tilemap/tile layer and multiple properties of each tile? I guess going through it like a 2d array would work, but the multiple tile properties is where I'm confused about what to do.You don't mirror, flip, rotate the tiles in the tile map, you do that to the tiles in the room. The tile map is just a palette of colors, except each color is a complete tile. tilemap_set_mask is for setting the mask, which is used for separating the index of a tile in the room from the properties of that tile.