You are correct, most of the receivers with two jacks are no different than using a y adapter as it is the same signal. Some of the higher end receivers coming out with the latest setup calibration offerings, are now incorporating 2 or more seperate subwoofer channels.
My Onkyo 3007 I got in Oct 2009 has two separately calibrate-able subwoofer outputs and I don’t consider it high end. I believe the 1007 does also and can be had for under $1K. I have even seen the 3007 occasionally under that price.