The pipelines created in blue ocean should default to logical settings for blue ocean and pipeline users.
The target audience is people using Jenkins for CI/CD. They may not know that they need to clean their workspaces between pipeline runs - they could reasonably expect that jenkins checkout will also clean the workspace. They may then get unexpected behavior due to workspaces not being clean before use or will have to include pipeline code to clean their workspace at the start of each pipeline run.
Instead Blue Ocean should add the "Clean Before Checkout" and "Clean After Checkout" options to multi-branch pipelines created in Blue Ocean (both are needed for truly good behavior). Also, the "clean" operation is git is not expensive especially when it is a no-op.