I just tested on a project that has a pretty big multisite network - clean up and root relative URLs are both working as expected.
Root relative URLs won’t work if your server doesn’t have a hostname. That means that if you access your site on a URL like http://127.0.0.1/ that relative URLs are disabled.
Clean up should definitely be working though. Are you seeing <meta name="generator" content="WordPress 4.1" /> in your <head>?
Hi again, thanks for taking the time with this for me.
It appears that the Shoestrap theme I’m using (Roots based) already does some of the features that Soil does and using the two might be causing issues for me.
I’m going to do some further testing with/without soil, make a few posts over on the Shoestrap forum and then post back here with any issues to make sure I’m doing everything correctly to save wasting any more of your time.