I definitely agree with the improvement in sound if you take the audio out prior to the effects board. It is definitely more present, clean, and natural. Quite inspiring.
The downside, of course, is that you loose the ability to use the chorus/phase/ensemble effect *and* you loose the ability to route the MG to the VCA. That's a stiff price to pay, but the improvement in sound (and reduction in noise) is worth it in some situations.
The noise gating circuit does sound bad. If you'd like to bypass the gating circuit but not loose the effects of MG-VCA, you can check out my mods (several were suggested and improved by folks here on this board) on my pages below:
Bypass the Noise Gate (or, as I call it, the "Post-Effects VCF"): http://synthhacker.blogspot.com/2013/07/polysix-bypassing-post-effects-vcf.html
Bypass C61 for Extended Bass: http://synthhacker.blogspot.com/2013/08/polysix-deeper-bass-bypass-c61.html
Chip