I use a Yamaha A6A AVR in my system which is set up for both home theater and two channel listening. It’s geared probably 90% toward music, stereo only, and the rest the occasional home theater. The AVR is only used as a preamp in stereo mode as I have a separate two channel amp that drives my front left and right towers.
Per Yamaha‘s instructions I set my speakers to small which keeps the LFE channels engaged in stereo mode and sends the bass to the subwoofers depending on the crossover level that is set in the AVR. The Yamaha’s room correction set that up and I tweaked it a little bit. Currently they are crossed over at 80 Hz. I run dual SVS SB 2000 subs.
With this configuration, in my room and my system it is extremely musical. I cannot tell where the subs are at all they blend seamlessly with the primary L/R towers (Focal Aria 926s). Generally I cannot tell where the towers are either unless there are some extreme left and right effects. The speakers just disappear into the soundstage as do the subwoofers and the soundstage extends well to the left and right and above and below the actual speakers. It is very enveloping.
Given my experience I feel it’s perfectly acceptable to run the subs through the LFE outputs. Between my manual tweaking and the room correction set up it blends everything very well. I would also think that you should be able to set a system up the same way as there’s nothing super special about my room but it is a matter of experimentation and tweaking.

