Firstly I'm no professional, however I've been doing my own powder coating (and numerous jobs for others) for several years now. I started with a basic DIY gun, deciding to "up grade" I made my own gun and haven't looked back since. I often powder over filler and have had no issues with it whatsoever using Dinitrol Alusoft 6030 which is a polyester filler with a high aluminium content. If my flattening out wasn't as perfect as I thought I use the first coat of powder as a filler primer, flatten it out to loose any marks, then re-powder. Unlike paint I can powder a part, rub it down as soon as it's cooled from baking, rub it down and re-powder straight away. No drying time, shrinkage problems etc. all in a few hours.
Rust coming through? The rust was never taken off the frame in the first place, this is purely down to bad preparation. It wouldn't have mattered whether the job was painted, powdered or plated, the rust would break through again. I media blast almost everything, don't touch it without gloves on once it's been blasted (and de- dusted), I've not had a single sign of any rust coming through and I ride my bikes all year round.
The biggest problem with powder coat is removing the damm stuff! Properly applied it sticks like the brown stuff to a blanket!
Polyester powder (most jobs on bikes and cars will be done with this) is softer than most paints, hence it is much harder to chip of, dent yes, chip off much more difficult. I clean very weathered / filthy powder coated parts with fine compound and wax just the same as paintwork, it shines up just the same as paint. If you do get a chip then do the same as you do with paint, small paint brush and a dab of paint.
You will never get the same perfect mirror like finish achievable with a top notch paint job, but that will have many layers of primer, and paint to achieve it (read time and money!). One coat of powder is equal in thickness to 5-6 coats of paint and that thickness of paint chips very easily.
If you're good at painting then tanks, mudguards etc. will have a better looking finish painted. If you're not so hot at painting then....... For most of the rest of the bike, properly applied (and prepped!) powder coating will look good and withstand knocks and marking a lot better.
Hopefully this link will work, I did this page quite a while ago when I first started powder coating and need to update it for my home made gun etc.
http://www.artfulbodgermetalcasting.com/12.html I painted the tank and mudguards on the restored Bantam, everything else was powdered. With the exception of the pin striping (painted on) every part of this bike no chromed (engine excluded) is powder, a project I helped a friend with
https://www.youtube.com/watch?v=ggKiAmT_rdM Obviously however you do the finish on your bike is up to you, but I had to write this as I'm a very big fan of powder coating and since I do it myself I know just how good it is............ Providing it's done properly!!
Colin