I wanted to follow up on this issue for anyone who may encounter it in the future, and will link it in the closed Github issue just for consistency.
Upgrading Bokeh to 2.1.1 got rid of the CSS issues that we were having. The next issue related to setting up Babel to run with a project-wide configuration. With Babel 7.x, a user should read this documentation to understand how it will transpile node modules.
Having set up the babel configuration with
"@babel/plugin-proposal-export-namespace-from"
the initial set of problems were resolved. Next, there was the following issue.
Uncaught ReferenceError: regeneratorRuntime is not defined
This was solved by following some of the advice in the following stack overflow conversation.
We now have @bokeh/bokehjs working in our custom project! Thank you team for the help.