I don't think it's that serious ...
Housing a boa and a ball python in split Boaphile (so long as the divider was put in there by the manufacturer) is no different than housing them in a rack together, really. There are plenty of people who house both BPs and Boas in the same room and in the same rack together. Their husbandry requirements are not that radically different (boas prefer an averagae of five degrees plus differential in ambient temps) and hooking them up to separate heating controls is not difficult.
IBD is also not proven to be air born, for the record.
However, Jeff actually builds "condo" like enclosures that would be better for this situation because I do believe he puts separate heating in for each individual "cage". Still, this is not really the best option. A ball python will need a bit more than 2X2 as an adult (at least a female will, and a male would be appreciative, I'm sure).
What I would do is one of the following:
Get this:
http://www.boaphileplastics.com/421coupe.html
When the Boa outgrows its side, get it its own 421D. The BP can remain in the original, or vice versa.
Buy two of the 421 coupes, keep the dividers in, let both utilize only one half of the cage as they age and remove the divider when they are ready.
Or ....
Purchase appropriately sized Sterilite (or equivalent) tubs, drill holes in the side near the lids, set them up with UTHs or strips of 3'' Flexwatt heating and hook it up to a thermostat. Then, get their permanent caging when they are older and better capable of dealing with the potential stress of a large enclosure.
Or ...
Purchase a rack:
http://www.boaphileplastics.com/rhinoraxx_ball_room.html
http://www.boaphileplastics.com/rhinoraxx_four_high_1986.html
http://www.animalplastics.com/
And then upgrade later (though a BP can comfortably live in the Ball Room rack as an adult).
I will say, I could put a young boa in a 421D and keep it comfortable with numerous hides and seclusion (they wander quite a bit in the wild), but this does tend to be easier for them to acclimate.
You're asking questions, so that is good. That's part of how research is done.