I managed to get rid of my phase issues by increasing the sub distance in my Denon's menu. My sub is 11 feet away but, through trial and error, I upped it to 19.

I do indeed have stereo direct but I find that even though the 80s have great low frequency extension, without the sub, they sound thin. Thin is perhaps too harsh a word but you know what I mean. I can't live without a sub now...even for just music.

House of the Rising Sone
Out in the mid or far field
Dedicated mid-woofers are over-rated