Hi,
As it is already cleaned I would probably paint it body color (with all the rust primer etc...) and then use a transparent undercoat on a wax basis, like "UBS 220" - guess it's german, but there will surely be something similar in the USA.
Ofc. it's not totally transparent but a bit brownish, but it's easy to identify any possible rust much easier and earlier as you could with standard black bitumen undercoating. Often it's too late then and bigger repair is needed as probably one or two years earlier, before the rust breaks through the black, dried bitumen.
The wax also can be applied in rather thick layers and hardens enough to keep off stone chips, at the same time stays smooth enough to "fill" holes especially when warm outside.