Hey there!
This behavior is logically intended, as LyraGame.target.cs runs ShouldEnableAllGameFeaturePlugins and magically enables any Game Feature Plugins in the project. However, we’re not happy with how this works in practice, and will be changing it for the Lyra Sample in 5.1, so that you can disable the GFP like a “normal” plugin. For now, the best way to test your project without certain GFP’s is to add "NeverBuild": true to your GFP’s .uplugin file.