Good question. It's too bad that there's no definitive answer. Both configurations have their pros and cons. I've heard that having a bay-res is bad because the seals break down over time. I've also heard that F&B kits are very hard to clear of bubbles. And there's much more anecdotal stuff beyond this. I choose a bay res because I wanted an easy way to maintain my coolant and thought it would look cool, which it does. BTW, whether your coolant becomes biologically active over time depends on the additives you use. Being free of spora isn't inherent to F&B set-ups. Also bubbles, will creap into your loop no matter what in that coolant evaporates through your tubing over time.
You might also consider a T-line. Lots of people swear by them. As for what YOU should use, well, the best thing to do is research all available options and decide on that which best suits you needs. Try to reject the idea that ONE way is the best way. Lots of people will try to peddle what they use as the only way in order to justify to themselves the choices they've made. Hell, you might come up with something that no one has considered yet.
As for me, I'm going to try to mix the functionality of both a res and a F&B kit by adding a check valve set on the pump return. Good luck in whatever you decide!