In the process of looking this up I determined the correct answer is to use the full local path in my dev environment, and add a comment in the code like
/** @define "get_template_directory()" "/home/myuser/mywpproject/wp-content/themes/mytheme" */
And this works for the subsequent references in that file in JetBrains IDE / PHPStorm immediately. Thanks to here by Jeff Behnke. I have not checked this on other IDEs. As this is a comment I believe it should not affect server side execution.
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