I've expanded these thoughts previously, you may have read them already.......
For a given set of twin / single equivalents, and in most caes before you add the aux, the heavier setup will alternate as you move up the HP range, simply down to the fact that most manufactureres make more then one HP variant for a given lump of hardware. "Twin X" for a given Hp will also vary depending on make
Drag is a similar argument as the gearcase sizes get bigger - my Clamshell has an almost identical sized gearbox to my old Suz DT25, but my Old Yamm 55 shared it's case with the 90! The drag argument goes up as the cube of your top speed. Crusie at 20 knots it's likely going to make negligible difference, but open up & do 35.......
Do you do your own servicing? If so the double service cost argument evaporates....
Slightly controversial thought ref. batteries etc. (and I say this ignoring any electronics you may want to keep alive) - rememeber a 60 is still in the "emergency pull start" bracket, so do you really need 2 bateries?
I have a single / aux at the moment, simply because the rib I bought had a transom cut-out and I didn't fancy rebuiilding it to take another Suzi. I also found a super lightweight 60 Hp to hang on it.
In a parallel universe, yes, I'd have gone with twin 30s / 40s. In answer to your "what to do with the aux?" Q - mine hangs on the transom, and is wedged in front of the frame & held in place with a bungee for rigid support & relatively quick deployment. I also use it to get in & out the marina or for a few mins at the beginning of the day each time to make sure it runs.