This does not directly address the question but is related (and related to the answer by ArianJM).
I came to this question as a result of a problem I just had uploading a new version to the Amazon Appstore.
The content on the referenced Unity Manual page from ArianJM has changed and (at least for version 5.4) no longer contains any information about Bundle Version or Bundle Version Code.
In Unity 5.4:
Bundle Version is now Version. This field is identified by the Amazon Appstore as Version name.
Bundle Version Code is still Bundle Version Code. This field is
identified by the Amazon Appstore as Version code. This field only allows numbers.
I am in the process of uploading a new version to the Amazon Appstore and although I updated the Version in Unity to 1.1, the Bundle Version Code was not updated and as a result was rejected by the Amazon Appstore because it was the same as the previous Bundle Version Code (Version code in Amazon Appstore).
I've since updated the Bundle Version Code in Unity - but could not update it to 1.1 or 1_1 because the field is strictly numeric - and so instead updated it to 2.
Which I believe brings us full circle to one part of the original question:
Is there a right way to number the bundle versions?
Although arbitrarily changing it to 2 in my case is clearly not much of a scheme - it is both different and higher than the previous number and, as such, works.
It's not much of a plan but the lack of current documentation by Unity addressing these fields - and the similar-but-different field names between Unity and the Amazon Appstore seems to lead to these ad-hoc decisions.