I see the assumptions you've made.
Menumanager works correctly with the current version of Bootstrap, which is 3.3.6. In the documentation (http://bootstrapdocs.com/v3.3.6/docs/components/#nav) you'll see that the anchor elements (not href, which is an attribute) do not have a class. They're all on the li element.
As you're talking about classes on the anchor element, it appears you are wanting to use the Bootstrap 4 alpha version? If you want to use an alpha version of software you can expect to run into issues with stable software, such as this plugin. I'd even go as far as to say that this plugin is incompatible with bootstrap 4 in it's current template style.
Secondly, the method outlined is the OctoberCMS way of over-riding plugin templates. It is not wrong, it is not bad, it is simply the way this CMS works.
After a very quick look at the Bootstrap 4 docs, the quickest way to get what you want to achieve is to over-ride the templates so you can get rid of the li completely, use the ul class on the nav element and the li class on the anchor. It's not going to end up with a useful user experience if you then need to pass this on to clients, and it will obviously require some work in the future if the component output changes in the future. In my opinion, you're better off forking the plugin and making the necessary PHP and template changes to work with Bootstrap 4. It has an MIT licence explicitly for this purpose.
I will be looking in to providing a switch between versions of Bootstrap and other popular frameworks in the future though, but as you need this now one of those 2 options will get you where you want to be.