The transfer function is only a scaler when all other things remain constant. You're going to be off when the enclosures take up different amounts of space in the vehicle. The transfer function of the vehicle is also dependent one the mass of air in the environment and not just the interior dimensions of the vehicle. Also, where you place the port, sub, and enclosure will all have a large effect on the actual FR. Another big factor in the transfer function is the natural resonance of the chassis and body of the car. This will also change when the different subs and enclosures are weighing down the car differently.
Theoretical graphs are useful but are to be taken with a grain of salt. They're also small signal parameters that will shift greatly when high power is applied. Just because there is a power input section does not mean it's adjusting for those parameter shifts due to losses in the EMF, suspension, or the coil heating up.
One of the most useful of the graphs is group delay and I didn't see you taking that into consideration at all.
I do believe in modeling subs before randomly designing an enclosure for them but you really need to be careful. At low volumes my IDQ in my room sounds exactly how it models up. When I crank the volume though, the low end begins to fade and the upper frequencies get boosted. My av12 in my car is the exact opposite. At high volumes, higher bass frequencies get a cut while the low end gets exaggerated. This is something that modeling programs cannot tell you.
To my knowledge, Unibox does not plot group delay for ported or sealed enclosures. I am not yet sure what kind of alignment I will even be using. And quite honestly I don't even know if group delay is something I'm going to even worry about. I assuming but I do think that the final group delay of the system (especially at low frequency) is going to be influenced far more by the cabin of my car than the theoretical group delay of the alignment and woofer I use. Furthermore, there is no guarantee that a sub with lower or lesser theoretical group delay will have lower or lesser final group delay once the system is installed in my car. And unlike cabin gain, group delay is not something I can measure with the equipment I have at this time. Since I can't measure it, I just assume it to be a constant because I cannot gauge or control it in any practical way.
The variations in parameters you speak of are complicated phenomenon and are very difficult or even impossible for even engineers with proper equipment to quantify (in an environment as complicated and changing as a car). Such a level of detail in my experiments will never occur, nor do I feel will ever be necessary. I am going to assume things like air mass (which depends on temperature, humidity and other factors), resonance frequency of the car, coil temperature, etc to be constant for the sake of simplicity. And also because even after I have finished my sub (and this goes for ANYONE who ever puts a sub in a car) these parameters will still be changing and I have NO control over it. Therefore, I will assume the transfer function to be a scalar and I am going to do my absolute best to make sure my tests are as true to the proper scientific method as possible.
Again, not once did I ever proclaim these graphs to be actual in car performance, like I said before they are simply starting points. I'm VERY well aware of the differences between theory and application and I'm equally well aware of the extra complications that come about in applications (things that you have mentioned). But I also know when and where to draw the line between parameters that will greatly effect performance and ones that I can ignore. Most of the parameters you have brought to my attention can be ignored simply because the difference they would make in final subwoofer performance is negligible to my ears OR because I cannot keep them constant in actual application. When you are driving your car and using your system, coil temp, car resonance, air mass, etc will all change as a function of simple and normally arbitrary things like window position, engine speed, gas tank level, average car temperature, ambient temperature pressure and humidity, road elevation or slope, passenger compliment, trunk utilization, etc. Hopefully you see the absurdity of even trying to consider such parameters when your experiment's purpose is to create a system for everyday use. You cannot take said parameters into account without creating completely unreasonable initial conditions and making for an experiment that cannot be carried out.
Also, at the very end of the day the system by which the success of our hobby is measured is completely subjective, differs from person to person and is impossible to quantify with numbers, arguments or theory. And it probably is not sensitive enough to discern the effect on your subwoofer when one of these parameters changes, nor is it consistent enough to do it on a regular basis. Hell, your first priority when in the car is concentrating on the road, not listening to music! And you know humans can't commit full attention to more than one task at a time!
Let me state this once more because I feel as though everyone is taking this the wrong way.
This thread was created ONLY as a medium to share my research into my car audio system. Many people don't seem to understand that this is JUST research and is NOT a proclamation of the performance of the (my) final product. I'm probably more aware of the fact that theory just about NEVER equals application in the real world than most people on this forum. The graphs and other information I presented in this thread are to be taken at face value and NOTHING ELSE. If you use them, use them simply as a guide or a starting point. That is it and nothing else!
Edit: If your going to bring car transfer functions into consideration when designing a car system, the ONLY thing you can do is assume it is scalar. Doing otherwise is impossible due to the complexity's of the variables that effect it. You need not worry about variables that you cant gauge, cant keep constant or will be continuously changing when under actual application. The best you can do is approximate average values for these values under operating conditions and go from there. The very, static, nature of a sub install also dictates that the transfer function be a scalar as well. There is little ability for you to compensate for a change in the transfer function after the sub is installed. Worrying about it as you seem to have done is not a reasonable thing to do under normal circumstances.