The 11'' idea sounds good. It would probably be cheaper, but a bit more of a hassle since I'll have to wire each shelf.
Is there any other reason why I should avoid using the 3''?
Yeah, it doesn't provide nearly the hot spot that females like and won't add any ambient temperature to speak of.
11X12 can be cut down to 10 inch so it covers a 1/3 of the tub and still provides plenty of heat and a decent sized hot spot to lay on.