Cargo Bars yep a pain in the neck.
I have had to remove them on six of the seven Hiluxes I have had,because I always fit canopies,& will not let the canopie fitters touch my truck,with a grinder. The professional fitters at ARB are very good at fitting the canopie though.
So removed them all myself as has been said already use protection behind cab to protect window & paint from sparks.
I found the easiest was to jam a piece oh masonite into the space betrween cab & tub.
Cut bars through with cutting wheel then remove the bar get extra pair of hands so as not to scratch the paint on the truck when it comes away.
Then grind down stubs, I fill the corner holes with fibre glass sand everrthing down nice & smooth hit bare metal with etch primer,primer undercoat for ENAMMEL paint finish you can get paint mixed to your color code to finish off.
I use enammel because it does not yellow & you dont have to compound it to get a shine If you add a little enammel add to it hardens the paint just like the latest epoxy finishes.
Just feather the edges (using 400 wet & dry)of where you want to finish it to use a mask down to a definate line.
Beauty of enammel it will go over all paint types just light sand them first.
I also used the same method to fill the holes where my roll bar was fitted,It would be very hard to pick the paint job & canopie covers most of it anyway.
CHEERS.