I own both and they're both very different guitars.
Both have the SE245 pickups and thick mahogany bodys with maple caps but that's where the similarities end.
The SE245 is 24.5" scale, has a wide/fat neck carve, and a wraparound tailpiece.
The Tremonti SE Custom is 25" scale, has a wide/thin neck carve, and a trem with an uproute.
Each guitar has a very unique feel but both are very comfortable, IMO.
If I could only choose one, it would be a very difficult decision, but I think I'd go with the Tremonti SE Custom.
The more I play the wide/thin neck, the more I really like it. I also like the option of having a trem.
But I strongly suggest you check em out for yourself.
They're both really great guitars, IMO.