there is no means of associating a CSS,
it is not possible to produce a valid article with the CSS squeezed into a <head> at the top of the Salesforce html.
Well, they're forbidding you to use the only two standard ways that you can format HTML content.
If you really want to use the HTML topic files generated by Help+Manual your only option would be to do ALL the formatting manually. Every paragraph should be formatted with Normal and ANY other formatting should be applied manually, by selecting the text and formatting with the Font and Paragraph dialogs. You will have to do this for every single paragraph and piece of text in your entire project.
The only alternative to that would be to not put the HM-generated content into Salesforce. Instead, generate a proper WebHelp output folder, put that online where you want to host it and link to it from your Salesforce pages.
If they won't even let you link to the WebHelp pages, then basically you can't use Help+Manual output because it means that Salesforce is locking out anything that is not created by them. Then you'll have to generate all the content directly in whatever editor/interface they provide.