No, heatmaps do not account for different designs of the same content.
In general, we recommend tracking different designs of the same content through versions, If you are working on big new updates for a specific content, create a new version of the content first:
That way you’ll:
- Maintain the heatmaps integrity for each version.
- Be able to work on the new layout for some time, while still being able to go back to the live page and make spot edits when needed. then publish the new version when ready.
Please refer to this doc for more information on working with versions: