Dear Winston,
I appreciate that you are a Level 10 contributor, but you are not in anyway contributing to solving the problem that I and others are experiencing. I know what you are saying and, originally - before iCloud Drive was a dedicated iOS app - what you are suggesting is the way it worked - and was expected to work. Now there is an iCloud Drive app and I know that selecting a PDF document and it trying to open in MindNode Pro is not expected behaviour. Moreover, I'm pretty certain that Apple is not expecting this behaviour either :-)
I use iCloud Drive to store different types of documents in folders dedicated to different projects. The folder is the starting point of the workflow - not the app. Frequently, I can't remember in what format the document I am seeking is in - did I create it in Pages, Numbers, PDF or whatever.... If the Drive doesn't function in the way that we expect what is the point of it! We might as well not have the iCloud Drive App and go back to the way things were before - pre-iOS 9.
Again, if anyone does come up with a solution - rather than a workaround - please post :-)
Regards
Chris