I did both rides last year. The main differences are far as I could tell were are follows:

5BBC version: It's earlier in the season, so chances are the weather will be a bit cooler. It's an insanely popular century, so it can be crowded on the shorter routes. The 100-145 seemed pretty manageable.

Glen's Ride to Montauk: It's a new ride so it's alot less crowded than the 5BBC version. It's also a couple of weeks later, so the weather is a bit warmer. Glen seems pretty obsessive about adding lots of little touches to keep riders happy... The routes are very similar. Glen added a couple of little detours to shake things up. I think he promised more route changes this coming year...

I rode and enjoyed both rides, but for me Glen's ride was a bit better. His staffers were very friendly and helpful. I'm sure it was a financial hardship for him, but I really liked the small feel of the ride. It's what I imagined the Montauk Century was like 10 years ago.