Please explain why in a 48+ table online tournament there is only one section rather than multiple sections.
In EBU BBO games any number up to 50 tables is in one section. Why would you like it to be otherwise?
Yes, I would prefer smaller sections with its winners then have overall winners. I would say 16-20 tables per section would be better; after all, it is all computerized so no issues whatsoever.
That's not how it would work: if you divided into sections there would still be an overall winner in each direction. It's one of the advantages of online bridge that there is no need to split into sections.