As you can see some of my modules have really long names, so having to constantly type it out can be cumbersome just to update the workspace.
Proposed solution
To my knowledge currently you have to save a new workspace with the same name to update it. I was thinking of adding an “update” button when in the Manage Workspace menu.
The Workspaces Plus plugin adds a Save current workspace command to the palette that simply saves the current state of the workspace you’re using under its current name. There’s no popup to have to deal with.
Not that I know of, but you could post a feature request on the dev’s github. The chance of getting that functionality added in a community plugin is probably higher than getting it added to the Obsidian core.