In regards to automating the FM voice. Speaking from the perspective of someone who loves FM/PM, has developed FM synths from the ground up and has extensive sound design experience on operator, FM8 and DX7s - the FM synth won't do smooth automation well, it's operators like to be set at sweet spots and left there. The synth won't really do expressive automation well. The only thing automation would be good for is, SFX and sample and hold type sequences. So I think the opportunity cost vs additional functionality wouldn't be worth it on the devs part. For the most part if you want variation on a sound just copy pasta and tweak the parameters.
I see what you mean about smooth automation, I was curious and tried FMHeaven and Toxic Biohazard and I hear some stepping artifacts when automating the mod matrix - I guess they do not interpolate smoothly on a sample-accurate basis (if those are the right terms - I have no idea what I'm talking about). Personally I don't notice the artifacting or aren't bothered by it. Example where I modify one of the modulators to switch between harsh and soft tones: https://clyp.it/dgwzbzpj.
But in the realm of FM trackers, it is common to see FX commands that modify the current instrument in real time (Operator level, feedback, Multiplier). VGM Tracker, Deflemask, BambooTracker and FMComposer all have this capability. And obviously it only modifies it on a per-step basis, so it's not intended to be smooth at all, but still allows more expression in instruments.