As it stands -- right now the aim of NodeBB is to replicate (with slight deviations) the core of that made forums great. That of a standalone community with its own content.
Now, this obviously is contrary to how integrated websites are nowadays, with content and comments tightly coupled.
The trick is balancing these two needs to deliver something that everybody can use, but even that is possibly an unattainable goal. If we swing too far one way, then NodeBB is no longer a forum, if we swing too far another way, we alienate potential admins.
I can say that we encourage cross-compatibility between standalone apps. For example, a website built in Calypso, with NodeBB bindings to periodically scrape content and automatically create topics based on new entries. This is do-able today (with some minor work).
I can also say that we don't want NodeBB to be a CMS. They are very different markets, with very different goals.
What I cannot say is how these views will change in the next 2, 6, or 12 months. It depends on a lot of factors, including feature requests and trends.
Now, as for #2, my personal opinion is that departing from the traditional "Category -> Topic -> Post" structure leads to confusion to first time users. Almost all users (and I realising I am generalising here), are familiar with that schema, and up-ending this is a risky move.
Discourse does not follow this structure. Their topics can have multiple categories, and their home page just shows a list of the latest topics. Whether or not this is successful or not is up to debate, but I will say that when I first visited a Discourse site, I was confused, as I expected to "drill-down" to a category of interest.