I would go with the AI version for a custom rifle
. Not strictly for the velocity increase though. There are other advantages to the AI or any improved case design, the AI is just one of the better fireforming systems out there if the chamber is set up correctly.
Most AI rifles will shoot virgin fireforming ammo into 1/2 moa or less at 100 yards making them extremely field worthy with virgin ammo if you get in a pinch.
The last AI round I range tested before shipping was a 6mm-06 AI. Loaded with a 70 gr Ballistic Tip in virgin 270 Win brass the rifle cut three groups at 100 yards that were in the .3"s!
The Ai case design dramatically limits case stretching as well which will result in longer case life if you load to pressures that will not open your primer pockets.
I would go with the 243 AI. You should be able to use factory 243 ammo with great accuracy if needed someday, a bit more velocity with 243 AI ammo over the standard. Longer case life.
Better all around really to some degree.
If the throat is cut true to the axis of the bore and chamber(which better both be on the same axial alignment!) I have not seen much difference between a short and long throat as long as they are cut to proper diameter for the bullets used.
I personally like the bullet to be held by the full length of the case neck, thats what it is there for so I see no need to seat the bullets out as far as possible to get those last 2 grains of powder in the case, as far as performance goes this is really pointless and at times will adversly effect accuracy.
IF your going to use 90 gr bullets for your light bullet, I would set the throat up to use those with their base right near the base of the neck. The longer 107s will seat below the case neck but when you want to use these different bullet weigthts there has to be some compromise and I feel seating the heavier bullets into the case a bit more is better then only seating the 90 gr pills 0.050" into the case neck.
Just my opinion,