Re: LFE vs. L/R sub channel...
I prefer the LFE single input. It was meant to be this way for discreet subwoofer audio.
The only advantage I have ever seen to the L/R type connection is exactly what you stated - the processor with the L/R sub outputs likes to use that connection for their DSP effects.
But when it comes to standard DD Pro Logic or DTS Neo Cinema, and discreet mixes, the algorithms were designed for a single LFE connection. When using the L/R connection and listening to discreet mixes, the L is the typical LFE connection and the R is the same signal but with an amplitude reduction to prevent phase cancellation when re-combined after reaching the subwoofer.
But when listening to the processor specific DSP, the DSP can create a special L/R sub mix that won't result in cancellations and thus the better sound through the built in L/R.
In my system I use a Y-splitter to send LFE directly to the SuperTower built-in 14" subs. This is all I need for powerful discreet surround mixes and then 2-channel signals I generally use the Stereo receiver setting or the Neo: Music setting which utilizes the LFE connection effectively.
So unless you use the processor solely for 2-channel music sources, I would use the LFE connection. It sounds better and cleaner to me. And you can say goodbye to the days of "non-issue" connections as the technology evolves even further. Makes life interesting but also confusing and stressful.