Daylight finally came and brought some snow. Oil change is now done (non-synthetic, thanks Mr Gibbs) and I closed the fuel tap and let it die out itself (thanks SkutFlut
I'll monitor the situation and update results/solutions in case it helps someone else out.
No further problems encountered, everything is exactly like it was last winter.
I have been turning the fuel supply off and letting the motor die on its own.
Also... another Yamaha owner told me that they had engine oil bubbling out of the filler hole at the beginning of this season. So maybe it is a feature.... Certainly hearing that made me slightly less concerned.