I have the PRS Multifit cases for all three of my SEs:
2012 SE Santana
2012 SE Custom 24
2012 SE Tremonti Custom

The PRS Multifit cases fits all three, but the Tremonti is a thick guitar, and the neck will not lay flat unless you put a towel underneath the back side of the lower guitar.
The other two guitars are a perfect fit and the necks lay flat as they should.

I took a chance earlier in the week and ordered the SKB PRS case from Sweetwater, and it arrived yesterday.
Wow, what a tank of a case.
Waterproof, air pressure equalization, TSB locks, and the neck of the Tremonti lays flat as it should.
Reason it does this I think is the cavity for the lower part of the guitar is around 2" deep, and the PRS Multifit case is around 1.75" deep.
This lets the thicker Tremonti sit lower, thus letting the neck now have full support.
I think if the PRS Multifit case was just a little deeper, the thicker guitars like the 245 and Tremonti Custom would allow the neck to have full support.

I was a little concerned the storage area has no fold down/snap lid to keep the contents from spilling out and into the guitar area, but Sweetwater assured me when the lid is down it for a tight seal on the storage area too.
The case also has built in wheels so you can tow this behind you like luggage.
It is pricier than the PRS cases, but I thought it well spent to keep the Tremonti in.

Here is a link to it with full specs:
SKB 3i-4214-PRS

Here are a few pictures.
Had the flash on, but the nice gray/black color of the guitar does not come through.
I think it is getting time to look for a new camera.

This will probably be the only SKB case I buy, as I am perfectly happy with the other PRS cases for the other two guitars.
May try the new 408 MT (on order, hope to have it in May) in this one though to see how it fits, and if I go somewhere to jam, may transport it in this one.

Tremonti in the new SKB case

Tremonti in the PRS Multifit case


SKB case at around 2" depth in the lower cavity

PRS Multifit case at around 1.75" depth in the lower cavity