Stoney:
That's a tricky question with an equally tricky answer. Here's my understanding:
You can use the component buildup method to estimate subsonic parasite drag of each component of the aircraft which you then build up to the total aircraft parasite drag. With that in mind you may be able to use this method to assess the drag of different canopies.
The first key relationship is:
Dp = f*q
This equation basically says that parasite drag equals to the equivalent flat plate area of the aircraft multiplied by dynamic pressure (.5, air-density, velocity-squared).
For the component buildup method you basically find equivalent flat plate area (f) for the entire plane by finding (f) for each of the components and sum them up. Essentially the greater the total (f) the greater the parasite drag. The equation for f for each component is:
f=Cf*FF*Q*Swet
where
Cf= skin friction coefficient (how smooth or rough the surface is)
FF= component form factor
Q= component interference factor
Swet = wetted area (total area exposed to the air)
Let's ignore Cf, Q, or Swet for now and assume they are they same for each canopy. With this assumption you can see that form factor FF then determines parasite drag. The larger the value of FF, the greater the drag.
Without getting into the details of the FF equations the relationship between form factor (FF) and fineness ratio is the following:

Diagram from Stanford:
http://adg.stanford.edu/aa241/drag/formfactor.htmlIn the diagram above K is the form factor. You can see that the greater the fineness ratio, the lower the form factor. The lower the form factor, the lower the parasite drag. That's why the fast-back canopy is said to be less draggy than a bubble canopy because as you have said the fast-back canopy fineness ratio is greater than the bubble canopy.
So it appears you have your answer. The fastback canopy is less draggy.
Well... here's the tricky part. Our assumption that we can ignore Q and Swet is not accurate because they may not be the same between the two canopies so you will need to factor these variables as well.
Interference factor, Q ranges between 1 to 1.5. You'll have to to look up resources to helpy you estimate Q for the canopies in question. Wetted area, Swet you'll have to calculate for each as well.
Oh, there are several different equations for FF for different parts of the airplane. Also there are different rules of thumb to use on scaling each equation depending on the shape of each aircraft part. Here's the FF equation for canopies and fuselages for your reference:
FF = (1 + 60/fr^3 + fr/400)
where fr (fineness ratio) is:
fr = l/d or fr= l/(sqrt[(4/pi)*Amax])
where
l= length
d= max cross-sectional diameter
Amax = max cross-sectional area for non-circular shapes
Tango, XO
412th FS Braunco Mustangs