Fixed with the help of Anthony Damico:

sample.brfss <- update( sample.brfss , one = 1 )
total_dataset <- subset(sample.brfss, (!is.na(agegr5) & !is.na(rfsmok)))
svystandardize(total_dataset, by=~agegr5, over=~one,population=popage)

Apparently SUDAAN doesn't age adjust over the variable sex if it doesn't
need to. The key to solving this problem is to add a variable=1 and adjust
over that variable if you want the total.

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