Like say I want to replace the widget definition (yes I know, possibly breaking everything!) contained in the file 'epi/shell/layout/LayoutContainer.js'. Is there any way of achieveing this in a straightforward manner?

You could do something similar to this quite simple in CMS 6 through the use of in cms6, but I doubt this will work considering al lthe widgest is minified into the huge "widgets.js" file in the shell zip file.