One multisite, or single install multisite?

I’m helping a nonprofit organization set up their site – which would consist of an online magazine at the root, and individual city blogs at nonprofit.org/[city].

I’m completely aware that setting up a multisite requires that the root site permalinks be prepended with /blog/. My aim is for the permalinks to be .org/articles/[post_id]/[postname] and I’ve set it up as so, having changed the Network Admin > Sites > / > Settings permalink structure. And it’s working so far. However, I’m unhappy because this feels like a hack-y, brittle fix.

Would it be more robust to set up a single install at the root (which will provide me total control over permalinks) followed by a multisite install in a subfolder? Or will it be better/possible to keep a single multisite, set up an /articles/ site, and have its wp_home set to root? Or is my current setup the best it’s going to get? I’m more than happy to make a couple of permalink structure sacrifices in return for robustness. The only thing is that “blog” isn’t going to cut it as we’re treating the site as more of a magazine.

Thanks so much in advance for any help!