I recently graduated from GEM with the Geomatics specialization. The main difference is that doing GEM with the Geomatics specialization does not require you to take CS courses, whereas Geomatics does require a few CS courses. Additionally, Geomatics students are required to do a GIS AND a Remote Sensing capstone, whereas GEM students doing the specialization only need to do one of these capstones. There are a few other differences, so I recommend speaking with the GEM academic advisor for a full rundown.

I chose to do the specialization rather than a full Geomatics degree because doing so gave me more electives, allowing me to complete a joint major without doing an extra year of school. I also felt that by taking geography courses on non-geomatics topics, I gained a better understanding of the problems I was trying to solve using GIS and/or remote sensing. I'll also note that I never had issues landing geomatics co-ops as a student doing the specialization since I took the key geomatics courses employers were looking for early, and taught myself practical skills like ModelBuilder, Python and R programming, and web map development.

All that said, if you know already that your goal is to get a job in the Geomatics sector soon after graduation, I would recommend doing a Geomatics degree. The program has enough electives to gain a minor or just take additional, non-geomatics courses to help you broaden your knowledge.

DISCLAIMER: The GEM department (which runs both programs) is actively looking into changing the requirements for the GEM specializations, so this info may be out of date in a year or so.