Am I misunderstanding this or are you?
My take is the OP is contemplating booking a cheap eco light ticket on AF/KL stock. DL operated flights will book into main cabin. His alternative is to book BE on DL.
There won't be C+ or F upgrades at all when he goes the second route. That is, it is better to have the chance of selecting seats at the time of booking and a shot at C+/F upgrade on the day of departure rather than not having those chances at all.
I thing you're actually getting what I'm saying, but dont realize it. I'm pointing out the only real drawback is that the flights will be coded as AF codeshare. Thus the main issue is that C+/F upgrades on DL metal will only be DoD. Thus the main drawback is that on domestic flights wont upgrade at the window. As long as OP doesn't care about that there's no drawback.