The issue that many people were raising is with regards to privacy (not saying your app infringes upon it in any way). If PWA deployment can ensure that the app truly stays offline, then that’s a good thing.
I personally like open source better, as it is easier to examine the inner workings of the app. It also helps tech-savvy users fix bugs and verify that it doesn’t do anything they don’t want it to do. Etc etc
Also, Electron apps can be sandboxed using Flatpaks for instance. Flatpaks aren’t perfect of course, but they do provide some guarantees. You can even use Flatpaks while keeping the source code closed.