Which is why the Operate Skill should really be a Specialist Skill, much like Common Lore or Linguistics, with players selecting an appropriate field within Operate (i.e. Operate (Chimera) or Operate (Grav Shute)).
This would kill the Operate Skill outright for any an all characters who don't want to be a designated pilot character but want to be able to pilot a few different kinds of vehicles.
Over here, we have a Vehicle Training Talent group. They are like Weapon Trainings, but for vehicles.
You aren't wrong, however realistic you want to be it severly hampering the designated driver (and as likely relegating them to an NPC) if there skils became redunant when a better tank became available.
I also like to think that an experienced IG Chimera driver would make a better driver of a truck or a tank (if they knew the controls) than some feral worlder with better coordination.
Simple answer is inflict a penalty for using an unfamilar vehicle. -10 for the rarer guard tanks, -30 for alien vehicles.
I can see the additional of a vehicle training group working as a more complicated method, there are more distinct categories in DH.