I can't find the reference, but the standard mobile ADE licence does not allow you to use ADE only for non-DRM ebooks. This isn't surprising, because Adobe makes money from DRMed ebooks. There must be a non-standard version of the licence that does allow this, because Amazon is using mobile ADE only for DRM-free PDFs on the Kindle DX.
It is relatively difficult to generate a MOBI/ePub viewer, depending on how faithful you want to be to the "standard". However, there are already 3rd party Open Source viewers available that may be "good enough" and being Open Source you can improve them if necessary. FBReader is the obvious example, but it isn't faithful to either the MOBI or ePub layout conventions. This isn't the only option, Calibre views MOBI ebooks by first converting them to ePub. This is the "Kindle" approach - view any DRM-free ebook so long as it is a MOBI. It would cost very little for Bookeen to setup an e-mail conversion service like Amazon's, although it obviously could not deliver ebooks directly to the device.
In fact, Bookeen could simply implement Calibre right on the Gen3. This is what
Savory does on the Kindle 2. It would not have to be automatic (like Savory): when you first click on ebook.epub Calibre is invoked to produce .ebook.mobi and then the MOBI viewer is opened. The next time, .ebook.mobi is already there. I added a leading "." because such files are conventionally "hidden" under Linux. The same process would work for MOBI ebooks when ADE is the primary viewer.