Retrieving Layouts via Metadata API (Salesforce CLI) Throws Warning:  

You do not have the proper permissions to access Layout

I came across the above warning, when I tried as a system admin (who has access to all layouts) to retrieve all layouts. I got most of the layouts, but still got two warnings (written above). I used the below command.

sf project retrieve start -m Layout

I wondered what was the issue, and I raised a support ticket. After an investigation, we found that there were two layouts, which were not possible to retrieve, since they exist in the org, but the feature that enables their access was disabled. 

The layouts in question were:

1. LiveChatTranscriptActive-Live Chat Transcript (In Progress) Layout
2. LiveChatTranscriptWaiting-Live Chat Transcript (Waiting) Layout

For our org, we could safely ignore them missing in the retrieval.