I have been enjoying dopus and will be taking the plunge to purchase soon. With that said, many applications that I use open on Windows Explorer instead of dopus. Take discord as an example. If I want to submit a file to a chat, I click the "upload file" button and it defaults to Windows Explorer.
I have a feeling I can't change this behavior because it is dictated by the application itself and may be out of dopus' hands. Is there a fix for this issue? Thank you.
There isn't a good way to replace those dialogs in Windows. People have tried but it causes more problems than it is worth.
Even Windows itself does not usually replace the old ones when they introduce new ones; programs have to opt-in in many cases.
But there are several tools which enhance the standard dialogs with extra functionality, including links to Opus (so you can quickly access Opus favorites or folders open in Opus windows, for example).
Here are some with forum threads. Not sure if there are others, but these are a good place to start if you want that kind of thing.
In no particular order (alphabetical, but one tool has two names so that's debatable 
- alphabetical by forum thread title, at least)