I'm creating a new theme and have noticed that the yellow color that appears as a hover property when editing descriptions is stored in the javascript (ajax.js). There should be a way to incorporate the tag in the teme CSS as this seems to be a theme-specific property. Will this be addressed in the future and is there a way around it in the meanwhile?

Yes, you are right, this should be themable. For now, you can override the value in ajax.js at line 207.