The inability to save the layout, including the zoom and position of the comment blocks, is a limitation inherent to Blockly itself, which was originally developed by Google. Blockly, as a visual programming tool, provides a powerful way to create code through drag-and-drop blocks. However, the focus of its design is on the logical structure and execution of the blocks, rather than on the visual or aesthetic aspects such as the exact positioning or zoom level of comments.

This means that while Blockly allows users to add comments for documentation purposes, it does not natively support saving or restoring the specific layout of these comments. The primary goal of Blockly is to ensure that the code represented by the blocks is consistent and functional, rather than maintaining the precise visual arrangement of the workspace.

If saving the layout and zoom levels is essential for your project, additional custom development would be required to extend Blockly’s capabilities. This could involve creating a custom wrapper around Blockly that tracks the positions and zoom levels and saves them to a separate file or database. However, such an extension would be beyond the default functionality provided by Blockly and would require significant effort to implement.

In summary, the limitation is due to Blockly's design focus on logical code structure rather than the preservation of workspace aesthetics. It might be possible to implement such features with custom development, but they are not available out-of-the-box from Blockly.