Thank you @statman for your reply!
I was originally thinking nominal could work and I would reference Alpha, Bravo, and Charlie, as 1, 2, and 3, respectively, but was advised not to do this by a statistics SME from work.
With regards to quantifying the three categories, I'm currently working to represent each geometry by its ellipsticity (fitting an ellipsoid through all the edge points and calculating ratios of the major and minor axis). I can't use volume because more interested in how the shape affects the combustion pressure wave, and ultimately the pressure magnitude I'm measuring. I could have the same volume but in a drastically different chamber volume, so volume alone won't help capture the effect of geometry. I'm also already using amount of fuel (measured in percent of chamber volume) as a factor, so using volume as a additional standalone factor would be considered double-counting.
To answer your last question, 6 pressure measurements were taken from the top and sides of each chamber and made sure to measure near the barrel entrance as well as near the igniter. Pressure between the chamber and ambient were fairly equal (+/- 0.5 psi).
All in all, I know that using Alpha, Bravo, and Charlie as as categorical factors of the character type in a least squares fit model is NOT the right approach. Yet, JMP allows me to do it. I just want to know what its doing in the background so I can point to it and say in my report "This is what it does, it's not good."