There's no crossover (that Atmel care about) between the two parts. Either you want the automotive, in which case you fetch the automotive dataset, or you don't, in which case you fetch the standard stuff.
You've argued yourself into a middle ground that doesn't really exist, and (I imagine) your volumes are nowhere near enough to make them care.
Silicon vendors, like any sane entity, want maximum return from minimum effort. A stream of support-intensive, zero volume customers, is pretty much the exact opposite... If it feels like you're swimming against the flow, here, it's because you are. It'll be hard work, and only you can decide whether it's worth the effort. Somebody had better be paying you for this time, one way or another.