Here is a temporary answer, that I'm not exactly happy with... Mainly because things aren't working how they should.
If you add "sourceMaps": 'inline' to the options listed in build/bundles.js AND ALSO copy the src folder over to the export folder, then you should get some sourcemap support. It doesn't seem to be working completely though for me, but it might be good enough to work with.
The fact that I tell the bundler to put the sourcemaps inline (and when I base64 decode the sourcemap it seems it is actually inline) but then I still have to add the contents of src directory to make it work doesn't seem right.
It'll look something like this:

I'm not sure if the issue is on the Aurelia side or the System Builder side though.