Just this morning I realized that I'm not following my own advice. I had forgotten that I actually do coat two different paints onto each other. After a few years of using Barnacle Buster (only) on my running gear, I came across a clearance sale on Pettit Hydrocoat Eco (white non-copper waterborne ablative paint) for about $10 for a quart. I decided to give it a try.
For the past few seasons, I put a couple coats of the white ablative paint over top the Barnacle Buster on my prop and shaft. It has helped cut down on the amount of hard growth, and also protects the Pettit paint so that I get more than one season out of it (I hate using spray cans, since over 50% of the paint misses the target.). I knew that a waterborne ablative would not attack a fully dried hard solvent-based paint, and if it failed to adhere it would be no big deal because it's supposed to ablate off anyway.
So far results seem to be pretty good. I do hire a diver once a year to do a mid-season de-slime on the hull, and he says there is nothing on the prop blades, and only a few on the hub, shaft and strut. At end-of-season haulout I typically see only a few barnacles on shaft and prop hub, which it much better than I was seeing with just the BB paint. I like having the BB paint as the bottom coat because of the anti-corrosive properties of the zinc (although the folding prop does have a very large anode).
So I'm being a bit of a hypocrite in suggesting not to mix paints. If there is a major problem, like incompatible solvent attack, you would probably see it right away (the underlying paint would start to wrinkle under the topcoated paint). It would create a bit of a mess, but nothing a rag soaked with solvent, or a wire brush, couldn't solve. Then you just start over again, having learned a good lesson. But it might actually work fine. If you decide to try it, I'd put the BB down first, then the CG, since you want the harder paint underneath the softer paint.