There is no telling why the special forces do anything, but I suspect it has more to do with standardization between SEALs and other special ops groups, together with the fact that the Gen3 Glocks have a long track record with special forces.
The Gen3 Glock is a fine weapon, and if that is what the operators feel they want and need, it is better they pick for themselves than some bloated Pentagon program which apparently the brass and even Congress seems unable to control.
That said, Glocks are still not perfect.
Go spend a little time over at Glock Talk, and you will find hundreds of posts about the same sorts of things you see here - light strikes, brass to the face, mystery marks, alleged cracks in the breech face, etc., etc.
We are lucky to have so many fine makers to choose from these days. The long track record weapons include the Gen3 Glocks, the Beretta M9, HK HK45 and HK Mk23, and the SIG Sauer MK25 and M11.
Since they value reliability above all else, if they need something off-the-shelf right now, and do not wish to have open competition, they are going to get something that is already on some government contract or approved list, or something that already has an NSN.
That likely accounts as much for adoption of the Gen3 Glock as anything else. As to whether their pistols will be "tweaked," I would imagine that as they are used, if "issues" are found, they will be "tweaked."
It should not be hard to find a SEAL with inside info to answer this since there seems to be a "former SEAL"* or other special ops guy (or a friend of one) in every easy chair these days. . . .
(I put in a smiley because I do not know how to put in an "emoji" for sarcasm.)
*I am not a SEAL, nor do I play one on TV.