I don't think your body guy meant he would shoot just base and no clear - that doesn't make sense. It would be flat and have no longevity. As has been said, he may put single stage in engine bay, just because it's faster for the shop. Often, shops add clear to the last coat of single stage, so maybe he meant no clear there (I hpe so!) I really like the idea of using a satin clear though. That could look good.
I've worked in shops for 10yrs and personally would NEVER use a single stage and B/C on the same car. As said, there can be color variables, sheen varibles and chemical varibales causing wrinkling or worse. Howevfer, in the negine bay it might be OK, because you can mask it off well. On my last project done at home I did the inners and outer in Single stage, with clear in final coat and don't like it - too much OP and not enough color sandability. This time I'm going B/C in and out. Just my opinions.