Saved Layouts should save all settings that affect how each panel in that layout looks and behaves, such as Copy Bible Verses settings, Visual Filters, and Search panel settings. Some such settings are saved (like number of columns, link sets and "follow"), but the implementation of saving panel settings with layouts appears to be inconsistent/incomplete. Other things which should be saved with the Layout but aren't include: whether the Interlinear panels were on/off, whether TOC panels were expanded/collapsed.
Example: I have particular Copy Bible Verse settings that I like to use for when I'm planning worship (for copying the Scripture readings to Word to print out for the readers). But whenever I load my Worship Planning Layout I have to reset my CBV settings to go with that layout if I'd been fiddling with them for some reason before. They do not get saved with the layout.
Steps to repro:
1. Save a layout (or open a saved one) that includes CBV.
2. Set the CBV settings to a style of your choice and a Bible of your choice.
3. Layouts > Update Active
4. Now change the CBV settings to something different from in step 2. Do not resave the layout.
Layouts > Reopen the saved layout by name
Result: the changes you made in step 4 stick
Expect: to revert to the saved layout as it was last saved.
Conclusion: These settings are not saved with the layout. They should be.
Same results observed with VF, Search Settings, TOC panel, interlinear panel. I suspect other Tool panel settings (e.g., Cited By) are also not saved with the Layout, but haven't taken the time to try them all out.