On the table of Emissivity, the listing for "clear silicone" is .080-.100.
The listing for "plastic", and mylar is plastic, is .95-.100.
So, on just a materials basis, it's close, and there is some potential for the silicone to have lower emissivity.
However, the surface finish plays a part in IR emissivity, and very polished or slick surfaces tend to have lower emissivity than rougher surfaces, so the mylar might have some advantage in that area.
In terms of color, darker colors generally have higher emissivity than lighter colors, so if the shelters are different colors, then it might make some difference.
My guess is that if the shelters are both light colors, it's not really an issue of materials because they are too similar in emissivity to really make that difference. If the cuben is light colored and the silnylon is dark, that might make the biggest difference.
I still think it would be marginal at most, and probably no real difference, in terms of materials. Conditions would be much more of a factor.