I agree. The second sentence sounds far more idiomatic to me.You can use 'the BMW' and 'the Ford' to represent all BMWs and Fords, but personally I think your second sentence sounds better.
Yes, Ford makes 2019 GT 40 with a starting price north of five hundred thousand dollars and BMW makes the Mini Cooper which starts at $22,900.00.If BMW made 1 car at 1 price, and Ford made 1 car at 1 price, then "the BMW" costs more than "the Ford".
But they both makes many cars at many prices, so you cannot compare "what the BMW costs" with "what the Ford costs", as sentence 1 does.
Sentence 2 fits the real situation better.
When I make a general comparison of car makes, can I use the singular form or better to use the plural one?
The BMW is on the whole way more expensive than the Ford.
BMWs are on the whole way more expensive than Fords.