Make users understand that a deep link is both to download and to use in the application

The main problem with that solution is that it satisfies two very different needs. If it is a simple link, such as "", there is not much you can do. Or change the name of the last part of the url to be clear, by clicking on the link that will join a group or install the application (such as "") or place a description in somewhere near that link, which should be stylized so that the user notices it.
Another way could be to use a button with a descriptive label.

However, both are not good solutions, but you need to communicate in some way the two different attempts.

I do not know his motivation to implement it that way, but I think he wanted to reduce the effort necessary to join the application. You can consider re-dividing those two functions, since it seems that the built-in installation function is not really necessary and may not fulfill its function.