Hmm, I see. I was under the impression that being allied meant certain minimum treaties would be in place? Like open borders?
a) The situation under the present, diplomacy-based system, is totally, utterly, and completely independent of the situation under the new treaty system. You can be at war with someone under the current system, and have an Alliance treaty signed with them. Treaties currently have no game effect.
b) Once the new diplomacy system is active, it will be perfectly possible to have an Alliance treaty signed with a realm and also have a Closed Borders declaration signed against them.
c) It is intended that certain combinations be mutually exclusive; however, they are not yet.