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If you don't configure it manually, `build.gradle` wins and will be used, `build.gradle.kts` will be ignored. But in the settings script, you can configure the build script name for each project including the root project. So if you configure `build.gradle.kts` there (or even `my-fancy-project.gradle.kts`) then that is what will be used and the `build.gradle.kts` will be ignored. If you want logic in both, you can also use one as script plugin from the other, but (non-precompiled) script plugins are ususally not worth the quirks they come with.

But imho that sanity check should be fixed. Actually you do not even have to have any build script for a project for example if you do the configuration in a different way, but that's not recommended and non-idiomatic.

Ah ok. So the build.gradle is selected by default. Thanks for the tip on configuring the build script name. That would solve my problem.