Will it ever be possible to block ads in these apps, possibly with root? Out of curiosity, why is this such a difficult task on Android, when it can be easily done on Windows and macOS?
IMO, it may not possible without patching/hacking APK files (e.g. what Lucky Patcher does) which would require root and can break apps.
Honestly, I'd look for alternative apps.
I suspect this is the beginning of apps doing things like this (e.g. double encryption). It'll likely become harder to block ads in apps in the future.
In my honest opinion, doing that could and can become a serious security risk. You're basically just asking for malware by doing this, especially from untrustworthy "developers". If you do this, make sure you research the modded app and the developer(s).