With you having Rhythm split by revit versions you may be able to have them in the extra folder or downloaded on a case by case basis. Then you could utilise the Packagemanager api to load the specific version you want to load into dynamo in the instance where it has just downloaded the files.
Here is a example of code that will load a custom folder then it will go through the folder and load each package it finds:
Note: You could probably re-use the first section as part of a checker to make sure the right dll/extension is not already loaded into dynamo.
Therefore you could do some Dynamo or Revit version checking then get the specific package from a sub folder or download it then load it in. Just hope on any further dynamo opening it does not cause any issues(we can hope 
).