In case anyone else is reading this because they are tempted to make their watch app work independently, then please think very carefully about it.
I enabled the WKRunsIndependentlyOfCompanionApp option a year or two ago because my watch app can work independently, so I figured it was worth doing. However the watch app is still best used with the iPhone app (e.g. configuration is easier on the bigger screen). As others have said, ever since I made the watch app independent then every time I release a new version I get complaints from users due to issues caused because either the iPhone app has updated and the watch app has not, or vice-versa.
The worst thing is that I can't roll that change back because of Apple's restrictions. For some reason it is a one-way change. This is why I recommend against making the watch app independent. Even if you think there is no need for a companion iPhone app now there may still be the chance that you may add one in the future (e.g. the bigger screen can be useful for configuration or analysis). So if you choose to make the watch app independent now then you may be setting yourself up for major problems in the future.
I do not understand why Apple cannot simply update both versions of the app regardless of whether the watch app is tagged as being able to work independently. Why would you want a user to have inconsistent versions? And if they can't do that then they should definitely improve the documentation for WKRunsIndependentlyOfCompanionApp. They need to make it clear that enabling that option will cause the watch app and iPhone app to get out of sync with every update, and that once you have made that change then there is no way back in future versions. At the moment that option looks innocuous but can be deadly.