Noooooo! Y cables are (with caveats) usable as splitters, but not combiners. Combining two signals requires a mixer (or some [usually active] circuitry).
The phase problem can be very real, notwithstanding that a Y cable is not the way to combine to signals.
I normally run in mono live, because I don't believe in attempting accurate stereo imaging in clubs or hotel ballrooms (not to mention that a stereo Leslie sim sounds whacked out when the mains are 30 feet apart). The best answer I have for running mono with Mainstage (though I would like a better one) is pick left or right at random, and just use that. On piano patches, for example, I would expect Left to be slightly bass heavy and Right to be treble heavy. AFAIK the Mainstage / Logic virtual instruments don't have a Left/Mono out (like my yamaha S90) or a Right/Mono out (like my Nord Electro). I don't know if those boards do anything fancier than just sending the channel whose output is selected, but one would sort-of hope so.
However, I recently did a session with the S90, in stereo, and we discovered that it's main piano had phase cancellation problems when we summed it to mono. So they clearly can't be giving me a left/right sum when I run from the L/mono output, because I don't hear phase cancellation then...
Cheers,
John