It... depends.
![Grin ;D](https://www.eevblog.com/forum/Smileys/default/xgrin.gif.pagespeed.ic.QVVz6XIT20.png)
If the different sections use expensive components, and there are dependencies between those sections, going for B seems more adequate. Otherwise you could waste a lof of cash in case one section doesn't work as expected.
OTOH, if the manufacturing time of the PCB is very long (can be if you're using very specific technologies), and/or the assembly (if it can't be hand-assembled) has a very long yield time as well, A may be the better option.
To best decide, do a compared cost and time analysis including the dependencies between sections if it applies, and a rough estimated probability of each section to be a failure (depending on complexity) and then decide based on this. This is actually basic project management stuff.
Now if there is no real dependency between sections or if the parts/PCB are not going to be expensive, or not going to take significant time to manufacture, there isn't much need to bother. In that case, do whatever you're most comfortable with.
A typical "6-sigma" approach would likely tell you to do A, but in case some parts can be excessively expensive, to mitigate the risk, possibly implement more than just one version of each section (for the sections that you know are more likely to cause issues), so in case one of the sections has bugs/problems, you have a fallback alternative and limit the risk of getting an unusable board. You get the idea. The main point with this approach would be to gain time, which can be precious. The extreme case would be when designing a new IC. Having wafers manufactured can be so expensive and so long that taking this approach is often the only reasonable option.