From The Omni Group's blog:
OmniKeyMaster is a simple app that finds App Store copies of Omni apps installed on your Mac, then generates equivalent licenses from our store - for free. This gives Mac App Store customers access to discounted pricing when upgrading from the Standard edition to Professional, or when upgrading from one major version to the next. Another benefit: since they don’t have to wait in an approval queue, our direct releases sometimes get earlier access to new features and bug fixes. OmniKeyMaster lets App Store customers access those builds, as well.
Tools like OmniKeyMaster have become quite common lately, as developers of third-party Mac apps keep struggling with the limitations imposed by Apple on the Mac App Store. Having new versions of apps every time a major upgrade is released isn't an option for many developers, and they are resorting to workarounds like this to have the best of both worlds: the Mac App Store's purchase system and the control on your own website and app updates. It's a trade-off, and, in most cases, the process is quite convoluted.
In The Omni Group's defense, their Mac App Store license tool seems easy to use and clever in how it finds all App Store copies of Omni apps on a Mac. Apple may not be interested in offering upgrade pricing on the Mac App Store, but developers find a way…or at least a viable workaround.