Is there any difference other than the throat sizes? Are the cup depths the same?

The 5GL has the standard large bore throat (.276" or 7mm) and backbore (429 in the Bach catalogue) while the 5GS has the .261" (6.63mm) throat and 420 backbore (same combo as the 6½AL, though the 5GS large shank backbore has a bevel). 5GL is a bit deeper than the 5GS but not as deep as a modern 5G. In fact, it's supposedly based on a Mt Vernon 5G owned by Mark Lawrence that is also shallower than modern 5G pieces, but not to the degree of the 5GS.

At one point I had all three. I passed the 5GS along and kept the other two. It ended up being too resistant for what I wanted out of my Holton.