First of all, I like MyTourbook, it is useful for analysing data from my Garmin Edge 500. However there seems to be some design problems.
Many linux users are installing software using their linux distributions package management system. For example there is AUR (Arch User Repository) for Arch linux. If the software is installed in such way, like most people do, there is no write permission to software install directory for regular users of the system. Therefore, it is impossible to update from 12.6.1 to 12.6.2 since the only possibility is to use the integrated downloader.
The integrated software update is mainly used for minor improvements and bugfixes because it takes less hours to do it this way instead of creating all installer packages, the OSX installer takes the most time to create it.