As far as I know, yes: You can apply different DiSEqC features on a Satellite by Satellite basis.
On both of mine, I use USALS and DisEqC 1.1 Port A for all but 28E and Port B to pick up a feed from a fixed dish for 28E.
Not tried 1.2 positioning, but I can't see why it wouldn't work for selected Satellites with others on 1.3/USALS.
Assuming you want to do this for trimming marginal Birds, if it turns out it won't work as you wish, you can always alter the stored Azimuth for the relevant Bird instead.