Actually there are many many similarities between turboprop and turbo fan engines.
Regardless, I can't vouch for the AE engines, but I have many engine manufacturers and different types of engines for each, and my commonality costs are still very good. I wouldn't worry about it personally, as the differences are probably only measured in the 10,000-100,000 range or less. Not much as that is per MONTH, not per week, and that definitely should be absorbed by the added aircraft.
To answer your question another way, engine commonality is based on (i think) only 2 aspects: Manufacturers and Model.
Hope that helps.