The reason they don't make shoe covers for flat bottomed shoes is because to keep the cover secured you need to run a strap around the bottom of the shoe. And with flat bottomed shoes, that means you'd constantly be walking on the strap, the strap would quickly get worn out and break.

Cycling shoes have a heel so there's a gap that doesn't touch the ground that the strap goes around. If you wear shoes or boots with a heel, cycling shoe covers would likely work as well.

However, the usual approach is to buy regular shoes that are not ventilated, and wear thicker wool socks inside of them. I was biking recently at around 18f, wearing the same Chrome Kurks I wear during the summer but with duct tape inside the shoe over the 3 holes they use on the side for ventilation. With FITS Medium Hiker Crew socks (3/5 for thickness):
Amazon - FITS Medium Hiker Crew socks

And my feet were very warm (honestly I was surprised how warm they were).