If you are customizing Chromium, just customize its Developer Tools feature, why bother separating them?
If you must separate them, you can add a build step that will either copy the files from the separate Developer Tools feature into the normal Developer Tools directory in Chromium, or change the path for the front end (I do not know where it is configured off hand).
In order to make Chrome use your customized Developer Tools feature, I believe you can use the --custom-devtools-frontend="path/to/developer/tools/front/end" flag.