Hmm gotcha I was afraid of that
I am aware of matlab and have some basic CAD skills myself but haven't worked with Matlab or other physical simulation software really so I'm not sure what kinds of other inputs you might need or what kind of data/formulas would be helpful. There are lots of explanations of the PID loop used for lots of applications in engineering where a system is attempting to lock in on a target with physical (non instantaneous/quantized/discrete) things but this one is especially geared towards calculating PID for quadcopters:
Regarding physical models of frames can find some of those on thingiverse.com the exact mass distribution might be harder to figure out though without weighing all the components etc.
Since most frames are carbon fiber and 4mm thick or more they won't have a lot of flex but there is always some amount of frame flex and resonance but yah not sure how big a deal that is to try and include in the modeling task.