There is not a setting in the editor or config files that I know of to do this currently.
You could edit the GameX.html.template file in the engine which is located here:
%install_location%\Epic Games%engine_version%\Engine\Build\HTML5
However, any changes will apply to ALL projects using that engine version, and you’d have to do it manually on every development machine. Unless you are working of the engine source, where the change could be shared.
There is a mechanism for project settings to be injected into GameX.html.template file. For example, if you look under the HTML5 platform settings in project settings, you’ll see and option to “compress files during shipping packaging”. This is injected into the template on line 37 in place of the placeholder variable %SERVE_COMPRESSED%. So theoretically, you could fork the engine source code, and add another parameter to inject a css filename into the template when you package a project.