Bubbles in the top coat seem to come from a void under the paint, which can be due to either painting over raw rust or pockets of solvent. If the rust is sound and converted to black, it has never bubbled on me.
To avoid solvent bubbles, allow ample drying time. That is an advantage us hobbyist have over body shops. I might prime and wait ~1 year before I get to the top coat (unintentional). In one case, I painted over Rust Destroyer primer and the top coat wrinkled a few places. It said to wait 3 days and I allowed 4 days, but the primer didn't dry enough in some corners (aluminum trim on trailer).
I always prime metal before applying fiberglass or bondo. Some apply it over bare metal or even rust, but I expect that will allow rust since water can migrate through fiberglass.
Re feathering in the repair, that is an art. I have seen real shoddy jobs, even from body shops, especially around rocker panels where they don't want to stoop. You must apply several layers of Bondo. First beat the metal as close to shape as possible, so you use minimal filler. That is an art. For rust-thrus, you already have the shape, but ideally would beat the surface down slightly so the filler is flush. Instead, I just extend it far out to feather it in. Never leave metal sticking up past the final surface or you will never be able to sand it flat. You may need to tap metal down after a few filler coats when you find you are sanding down to metal.
Plastic spreaders work for small areas up to ~3" across, but for larger areas they flex too much. I use ~12" wide metal drywall blade to smooth large areas. Having worked with drywall mud is a big step towards Bondo work. Once, I re-did a dented door which turned out wavy in the first repair. I used a 1" wide steel strip to spread the Bondo flat across the whole door. It looks great now and the paint hasn't cracked in 15 years. The final word is the reflection of parking lot lines in a gloss clear-coat.
Bondo claims 5 minute working time, but I get ~2 min after mixing and that is after chilling it. Count on 2-3 swipes with the tool, then don't touch. Lucky if you can work on 2 spots with one batch. Clean your tools quicky with acetone. I mix it on plastic lids. After 10 minutes, use a wood rasp (like wood plane but cheese-grate bottom) to grossly shape the surface. If not, you will sand forever. I usually make ~4 passes w/ Bondo, sanding between w/ 240 grit and don't need the grate after the 2nd pass. To fill remaining pits or glitches, use the red laquer filler that comes in tubes. Some people spray black paint on in-between Bondo coats and sand to check flatness. I shine a light across the surface and run my fingers over the surface.
Re feathering in, all edges of the Bondo should appear translucent, gradually changing from opaque to nothing over 1/4" or more. If not, you have will have a visible edge that will show in a gloss top coat.
