That's what you want isn't it ?
So my question is............do you want dimples filled with rust or dimples to fill without rust in them ?
I'd say it's a pretty straight forward answer isn't it ?
This is what automotive filler is used for in this instance, or just straight paint it as you really won't see that part of the machine once to start using it again on a regular basis again.
Note these later units had a hole drilled into them ? this was for hanging purposes during the powder coating process, bit rough isn't it ?
I'd zap it up with a mig welder and grind it flush then paint over it so it's not seen, just my take on it I guess.
Cheers,
BB.
PS. It's a pretty good result isn't it and much better than using so much elbow grease ?