There is a third option and to me is likely the better option.
The themes are applied by default but there is somewhere to easily disable it on a a per app basis by the user and not by the app developer.
This makes it so some consistency is the default option but if something breaks then you can disable it. Maybe throw in some user education if you are really worried about this.
Edit: Also to be clear I don't really agree with the article. I understand some of the points it makes but considering downloading an app and it having a different UI is a frustration for me I would be very happy if on my iPhone I could somehow overwrite parts of that UI. (Ultimately right now I just uninstall it)
I think the UX of requiring users to opt out of untested and likely broken themes on a per app basis is bad.
I think an opt-in via prompt on first run (or whatever) is a better experience since it makes the distinction clear in case stuff breaks and provides an opportunity to warn users about potential breakage.
The themes are applied by default but there is somewhere to easily disable it on a a per app basis by the user and not by the app developer.
This makes it so some consistency is the default option but if something breaks then you can disable it. Maybe throw in some user education if you are really worried about this.
Edit: Also to be clear I don't really agree with the article. I understand some of the points it makes but considering downloading an app and it having a different UI is a frustration for me I would be very happy if on my iPhone I could somehow overwrite parts of that UI. (Ultimately right now I just uninstall it)