The standard Floquil paints are laquer based. The Scalecoat 1 paints are alcohol based. Floquil has also offered water based acrylic paints in the past. I'm not sure, but I think Scalecoat II is a water based acrylic. The water based acrylic paints are compatible, and can be thinned with water or denatured alcohol. Some can be thinned with isopropel (rubbing) alcohol, but I've found a lot of the acrylics will shock when you try to thin them with isopropel, so I use denatured which I buy in gallons at the local home improvement store.
The laquer based paints and alcohol based paints are not compatible, but if you let the Floquil dry completely, you can paint over it with the Scalecoat without problems. I'm not sure it will work the other way. You need to be careful of the amount of scalecoat you shoot, because alcohol is one of the products regularly used to remove paint. In fact when you read of people using automotive brake fluid for paint remover, the thing in the brake fluid that disolves paint is the alcohol. Also Scalecoat never dries to the point that it won't disolve when hit with alcohol. A friend of mine who used to be a custom painter before he went to work as quality control manager for Athearn, used Scalecoat exclusively for his custom painting. He always made masks for his paint jobs so no color of Scalecoat was ever applied over another color of Scalecoat.
If the caboose red is too dark, you could respray the caboose with a thin wash of Floquil reefer white thinned about 10:1 with thinner. You might experiment with a piece of scrap plastic to see what you need to do to get the color about right. Since red is the worst color for fading when exposed to sunlight, almost any shade of red that is too light can be correct, but too dark is not so good.
I hope this information helps you.