You've used the UI to create the package (File menu). The UI way of creating packages is pretty simple. It creates a package that ensures will open in the oldest version of the software that reads packages, as well as the current version. Current version is obviously important because there might be something that only exists in the new version and you want to be able to maintain that when someone opens your package in said "new" version. In short, it's all about backwards compatibility as you may put your MPK on the internet and who knows what version of the software someone has who tries to open your package.
If you want fine grain control over what version ends up inside your package, use the Package Map geoprocessing tool. The tool has a version parameter. You could build a 10.6 package only, thus having 1 folder and limiting support to "newer" versions.
As for a Runtime package creating only a v101 folder -- you're building a package for a very specific application (Runtime). Yes, it's usable back in ArcMap, but by you selecting the Runtime option, you're saying this package is meant to be used in a Runtime application. Runtime has it's own list of features it supports. The "contract" that the v101 package and the Runtime application have is the app understands the contents of the v101 folder. The ArcMap and Runtime teams have worked out the supportability, thus it's maintained this singular v101 folder despite the version of ArcMap and Runtime you're using. (The amount of work to increment something as seemingly simple as a folder version number is way beyond what anyone would ever imagine, so if it doesn't need to happen: it doesn't)