The short answer to your question is no; or rather, Yes, but only in the way that you've already discovered.
Color schemes can only apply foreground/background colors to scopes as well as bold/italic font weights. So assuming that there is a specific scope detected by the syntax you're using that is used for the things you're trying to highlight, the only thing the color scheme can do is alter the background color to make them visible.
The only thing that can render white space natively is the draw_white_space setting, which at the moment only allows you to turn it off everywhere, turn it on everywhere, or turn it on only for selected text. In this case that doesn't really help.
There are possibilities for something like this in the plugin realm though (these examples can be tested by opening the Sublime console with View > Show Console or Ctrl+` and entering the code in there; they also assume that you're using the default Markdown syntax):
view.add_regions("whitespace", view.find_by_selector("punctuation.definition.hard-line-break.markdown"), "comment", flags=sublime.DRAW_NO_FILL)
This will cause all of the hard line breaks to be outlined as if they were find results; the color is selected by the scope (which is comment here); that would make them visible without making the whole character position have a background color.
view.add_regions("whitespace", view.find_by_selector("punctuation.definition.hard-line-break.markdown"), "comment", "dot", flags=sublime.HIDDEN)
This will add a dot (colored as a comment) in the gutter for lines that end with this scope; you can also combine this with the previous example to outline them and also call attention in the gutter.
style = '<style>.w { color: darkgray; }</style>'
content = '<body id="whitespace">' + style + '<span class="w">··</span></body>'
phantom_set = sublime.PhantomSet(view, "whitespace")
phantoms = [sublime.Phantom(r, content, sublime.LAYOUT_INLINE) for r in view.find_by_selector("punctuation.definition.hard-line-break.markdown")]
phantom_set.update(phantoms)
This uses Sublime's ability to apply inline HTML phantoms into the document in order to inject a small inline sequence of two unicode center dots immediately between the actual whitespace and the text that comes before it. Here the content can be what you like if you can generate the appropriate HTML; we're just applying a color to the text in this example.
A potential downside here is that the characters you see in the inline HTML aren't considered to be part of the document flow; the cursor will skip over them in one chunk, and they're followed by the actual whitespace.
The result of this example looks like this:
Going the plugin route, you'd need an event handler like on_load() to apply these when a file is loaded and on_modified() to re-update them after modifications are made to the buffer. There may or may not be a package that already exists that has implemented this.
