Designing a communication software with audio/video chat starts to have a lot of chat controls and the UI starts to get cluttered. I am wondering if getting rid of application's volume control and depending on master volume control of the computer is a good UX or not.
Unless your application will be the only application running (for example, you are designing this for a kiosk) then I suppose it can work, but for all other applications this is not a good idea for many reasons:
As a user, I would like to mute only your stream, without muting the entire system; which is not intuitive at all for most users. It is possible with a few right clicks on Windows (haven't seen this option on macOS), but it is not intuitive at all.
Why work against the tide? It has become the de facto standard that video players have a play / pause or stop button, a timeline / scrubber, and a volume control in that specific order at the bottom of the widget. Your users will be accustomed to see things that way.
You can hide the control bar when the cursor is not in focus on the video stream, and only display once the mouse moves over the stream - this is often how full screen media applications work, but it doesn't mean you can't try it as part of a larger user interface.
I agree with @BurhanKhalid answer. I just wanted to point out an idea. Apps could be left without individual volume controller if none of them have one and all relied on the system volume controller (a single controller). Apps would still need a mute button though.
This gives the user less control but a simpler experience. If I am not wrong this is how it works in most phones.