I don't have Audyssey, but I know "running it once" is probably overly optimistic:
Anyhow, yes, I have the sides angled in, aimed right at MLP. I don't have the center tilted, but the horn is high enough off the floor that I don't have any problems with dialogue (and I'm not anal enough to worry about "floor bounce" from the woofer).
I'm sure you'll be able to find some way of keeping the Atmos speakers on top; as you can see, I have something on top of each.
I had the ports plugged for a while, but measurements with REW lead me to unplug them. Sorry, I don't remember why, but I still love them as they are.
My first generation Pioneers and DIY Fusion 8s are in the basement (and on Craig's List, actually).
I have the xo at 100. Without measurements, you probably won't be able to evaluate the difference. I'm sure it depends on the subs and the room and a million other things.
I am sure, however, that you will enjoy them, especially if you're a value/price fan.