with the maps and paths now specified here can we remove the corresponding config from scriptLoader?

No. The ones in the scriptLoader.js are client-side and they happen before adapt.min.js is loaded, the mappings from the compiler happen at the top of adapt.min.js, after those modules are needed. Oftentimes external libraries/ files will expect jQuery at minimum and will need access to jQuery before adapt.min.js is loaded.

We will be able to remove some of them as we move over to node_modules, specifically: regenerator-runtime, core-js, react, react-dom, html-react-parser and semver. The others will be more difficult.

ah, of course, though is the scriptLoader map used at all?

The only use I saw was spoor's offline_API_wrapper.js, but I think that has recently been moved into compilation, right?

The map properties are used heavilly in adapt-devtools. The paths section is used further down the scriptLoader.js to load the foundational libraries+templates and some of those libraries are used by name at various places throughout the core and plugins.

map

  coreJS: 'core/js',
  coreViews: 'core/js/views',
  coreModels: 'core/js/models',
  coreCollections: 'core/js/collections'

These shortcuts were mostly removed when we switched to babel and jsdoc, both of which really only work correctly with resolvable file paths.
#930

Effectively, when core is updated to switch to node_modules, we can also drop the scriptLoader.js directives, where reasonable to do so, considering backward compatibility and load order. jQuery, jqueryMobile, underscore, backbone, handlebars and Modernizer will be most difficult I imagine. imageReady, inview and jquery.resize are libraries I made, so they should be quite easy to integrate into the core. bowser, scrollTo, requirejs and velocity I haven't analysed yet.