What is the best method of syncing photos from iPhone to (windows) desktop?
My issue ended up being driver related, what tipped me off was that the iPhone wasn't browseable in 'This PC' with DCIM available, so the photo app must have been using some alternate method of transferring the files.
Downloading the official drivers to make the iPhone show up as a removeable storage media device, allowed Windows Photo's to transfer all of the files successfully.
The files didn't seem to be packaged with iTunes as explained in https://support.apple.com/en-au/HT204095
So I ended up installing iTunes normally, checking for the drivers and not finding them, installing iTunes from the windows store, then following the instructions to update the driver in device manager.