When using a "collection of images" tileset where some of the images span multiple tiles, is there any way to affect what tile is counted as the base tile?

Say i have a 3x2 mountain image that spans 3 horizontal x 2 vertical tiles plus little bits that overlap out a bit. Tiled considers it as 1x1 based in the bottom left of the image. Can I have the base anchor tile be the upper left, or tell it the image is really spanning 3x2 tiles and have the CSV layer output reflect that?

As already replied on IRC: No there is no way to do that. You will need to handle the offset when loading the map.