Zitoon, Your right. The licences you earn are approved and issued by the UAE's GCAA. You'll hold an international licence issued by the UAE (which is an ICAO signatory state). You wouldn't be able to start flying for a European carrier without holding a JAA licence being issued by a JAA member state first.. I think..
The fact that the course is based on or compliant with the JAA system/syllabi might signify that the conversion from your GCAA to JAA might be nothing more than an administrative matter.
Zone 2 Alt, I think they are basically offering training towards the issue of a frozen ATPL on an integrated course, BUT with dual type rating thrown in at the end. I know they don't or house any level D FFS, but I reckon a partner UAE based TRTO such as CAE-Emirates will probably carry out the jet transport type rating element of the course.
The Eclipse EA500 type rating will probably be conducted in-house as you'll be studying the ins and outs of the aircraft and actually spending some 50 hours in it.
My two cents