With some (older) games providing both Linux-native and Windows builds, sometimes, it's beneficial to run them through Proton, other times natively. For example, PayDay 2 has a native and Windows version that both work on Linux, but one might work better than the other for a specific use case (modding, graphics API, update status, etc.)
This is also useful for benchmarking games that have different versions on a release.
With some (older) games providing both Linux-native and Windows builds, sometimes, it's beneficial to run them through Proton, other times natively. For example, PayDay 2 has a native and Windows version that both work on Linux, but one might work better than the other for a specific use case (modding, graphics API, update status, etc.)
This is also useful for benchmarking games that have different versions on a release.