At my previous company we edited apks to add performance trackers. We modified the dex code directly. It was not easy, but it is possible. Some apps are obfuscated, which makes finding libraries hard. But a principal we used was to look for where the app called into the system code, especially around URL requests. So you could look for all calls to the system network libraries, and identify which ones were calls to tracker systems, and no-op those bytes.
But, it’s probably much easier to just use the adguard dns server.