If this is the case, is there no way of exporting a whole tree including photos into some other sort of file without this fiddly keeping track of lots of photos?
As soon as the translation of GenoPro is complete, we will start working on a collaboration system. Our collaboration system will sharing and editing family trees with pictures over the Internet. Our collaboration module will be a great feature for people like you.
Same names yes but not necessarily the same folders. You can use the Tools / Relink Pictures to switch folders.