Given how much Star Trek, Star Wars, Marvel, and DC have changed their own universes I don't think there is any real harm in using any of them, or all of them combined, for your own campaign. Lets say you're going to set one in the DC Universe, but which one? One based on Batman/Superman/Justice League Animated series, or the DC Extended Universe, or the Dark Night, etc. For Star Trek what time period would you be playing, the original series, the Next Generation/DS9/Voyager, Discovery, or the Kelvan timelines?
Of course if you're doing an Agents of SHIELD campaign I recommend using the Horror Hero campaign book.