Creeper, the last part to the scope, as in 3x9x40 does indeed refer to the objective...the eye could be any size.
I have a LaRue EER mount with an Accupoint. The EER pushes the scope far enough forward to *barely* clear the front of the 40L I have on that rifle, so that all of the eye is forward of any part of the 40L. Based on that, I don't know that a longer scope, coupled with a LaRue SPR mount, would work the same way....I dont' think it'll get the scope far enough forward.
I know that ARMS #22 high rings will clear a reg ARMS 40 with a Simmons Aetec, which has a fairly big eye, with no trouble. Check out how high the LaRue Classic High rings are...that might solve your problem.
Another, much cheaper option, is to grab yourself a Yankee Hill riser/extender...$35. That will raise the scope and allow you to move it forard as well, taking the BUIS out of the equation, and use medium height rings to boot. They have a 5" and a 7". I would recommend the 7", just in case you need to spread the rings out on the scope more. You can use 2 of the YHM thumb screws to secure it...if you tighten those down tight with a quarter, they'll be tight enough to secure the mount, but you'll be able to take it off fairly easily when you want to go back to your Eotech.
Now, I have no idea how "repeatable" the above setup is...I have it a on a lightweight carbine build, but I've only tried the red dot on that rifle so far. When I get to the outdoor range at some point, I can give you a much better idea how this works in reality.
check out the pix in this thread...especially the one by Lost.
www.ar15.com/forums/topic.html?b=3&f=18&t=246861