I'd say that depends on a writer's intention. 超空間 is a special term, so feel like that we have no clear and familiar definition of it. But native Japanese speakers would usually think of the latter one, a higher-dimensional space.
A lot of fields have a lot of kanji compound words they made up temselves that they regularly use. This is likely one of those as well. You'll mostly find them in articles and scientific writings, and not in dictionaries. That is why you should use a copus of sorts to look in what kind of contexts it is used, and deduct a meaning from the context. Here's what I found on Weblio: https://www.weblio.jp/content/%E8%B6%85%E7%A9%BA%E9%96%93
What is the terminology of 超空間 (superspace), and what is it referring to?
I have been pondering this question for about a year now, and when looking for an answer today, I couldn't find anything. Is 超空間 referring to superspace in a mathematical sense (i.e. a space with more than four coordinates; an infinite-dimensional space), or is it referring to a higher-dimensional space?