As far as I'm aware, the only way to generate/update a report lay-out in the AL VS Code extension is to set the `generateReportLayout` to `true` in the settings.json and recompile the AL package. This method tends to lead to many - semantically pointless - changed files in the Pending Changes pane, due to minor formatting differences between lay-out files created/updated by the AL compiler, and files that were edited using e.g. Report Builder. 

My suggestion is to introduce a contributed VS Code command that is active only when a report object is open in the active editor tab, and that updates (only) the lay-outs that are associated with that report object. 

Alternatively, the command could be permanently available in the command palette and, upon invocation, present a list of reports from which the developer can select the report to update.

Yet another alternative might be to leave the lay-out files unchanged unless there actually are semantically relevant changes.