Paint over Bondo

I have a truck hood and top off a 1989 truck my kids bought that looks like a Cheetah scratched it. A MoPar parts guy suggested I use OSPHO, after sanding just as extra rust insurance. I used epoxy primer before a bondo with aluminum. Next I used primer. I'm finished painting, but there are high and low areas from some views, that seemed to appear after I finished. It's a 20 foot paint job for sure, but I feel the body is protected. Any advice for next time?
Be careful with OSPHO as it should always be neutralized that is wet it again let it stand awhile but while wet, rinse with water. Some epoxy primers can react to it and sometimes months later.
I use OSPHO to kill rust where I have welded, and on metal that has pitted, etc. Good stuff but be careful with reactions!