I stumble upon a new software (for me) at work for stitching (and specifically, flat stitching).
It’s called ImageJ. I play little around with it (the Fiji flavour, which contain stitching plugin). I found the Pairwise Stitching very effective, but as the name imply you can only do it by pair so if the collection contain a lot of image it tend to be click intensive.
There is another plugin
Grid/Collection stitching, which seem very close to what @bieber was looking for. You can feed the plugin with image in a dedicated folder and choose from the various way of ordering them to help the plugin do the stitching. I have to admit that I didn’t succeed to make it work with the provided files, but I didn’t spent much time on it either.
Hope this will be worth looking.