I think you're right, that /Packages is probably the better choice rather than /Packages/User. And if that setup lets you have convenient access to overriding any of the theme settings easily then it makes even more sense.
I took a gamble on my interpretation of what the "User" folder might be for, and from some of the discussions I've had, it looks like it's more for the individual users customisation, rather than general, third party / non-core (aka not shipped by default) customisations.
There were a few points raised over on the GitHub page about it: github.com/buymeasoda/soda-theme/issues/10
Perhaps Jon, you'd be able to confirm, should the theme be moved to /Packages? Is that the preferred location for things like a UI theme?
Suggestion: One of the ideas for circumventing pathing issues with theme assets could be to path from the theme file location down relatively, rather than making paths relative to the fixed /Packages starting point (more details on the github issues page). Then it wouldn't matter if the theme was placed directly in /Packages, or /Packages/User as the assets would always be referencable.