1. Understand first, it's all Debian underneath, so some packages certainly will work cross-platform.
2. Understand that when Ubuntu starts making modifications to Debian, those modifications could break some things and make some things incompatible, so you should prefer Ubuntu packages first, if available.
3. Likewise if using Mint based on Ubuntu, you should prefer Mint packages, if available, and then Ubuntu, before considering Debian packages or debs from other sources. If using Debian edition, prefer Mint, then Debian; there isn't an Ubuntu version unless they've changed something, and they are likely changes you don't need.
4. Understand also that Mint is a small distribution, without the manpower to maintain every single package. They are responsible for their own improvements and contributions (the Mint Menu, Mint Upgrader, Mint Installer, Mint tools, etc.), and they can test other packages and include those that are compatible in the repos. But there's no guarantee that every single thing you might want will be available for Mint.
But in this case, you should realize that the package in question is not coming from Mint developers, maintainers, or repositories. You are getting it from VirtualBox.org, so it is coming from someone at Virtual Box, or Oracle. I don't know why they would upload an Ubuntu package to a repository they have set up for debian, but you would have to ask them. It may simply have been a mistake. It may also be this is one of those pacakges which works fine on either, and they just didn't bother renaming it.
As for the confusion of the process generally, I think ideally more of these improvements would be done in a way that was fully compatible with Debian, so that they could work alongside existing packages and not cause breakages. But understand also, that companies like Canonical or Oracle are sometimes naturally a bit less concerned over whether their customers have full compatability with free alternatives. This is not a criticism, both are great companies, and have contributed a lot which we should appreciate. Just remember, when you ask for help at Virtualbox, they really don't have to support Mint at all, much less Debian Edition (which is currently maybe 10% of Mint).
Also, there is a complete "free software" version of VirtualBox available, labeled VirtualBox-OSE (for "open source edition"), but this is one of those cases where you are likely better off going to Oracle (as you have) instead and getting the latest. Just understand the usual tradeoffs there, you are getting newer versions, with more features, but also mistakes and bugs and things that haven't been as fully tested and vetted.