Schools sometimes double up their job ads in ways confusing to applicants. For instance, a school may identify a single position as "Instructor, Assistant, Associate, or Full Professor," or as "Instructor/Assistant Professor/Associate Professor," signalling that they would offer a title based on the chosen applicant's experience and credentials. Alternatively, they may have multiple positions open but file one job ad. (It could be a deliberate cluster hire, or just a matter of how the department filed the positions.)
What you're describing is a blend of both approaches - hiring for positions of multiple ranks in one institution in one ad. There is no industry standard for how applicants should handle this exact situation. Instead, I'd advise treating each position like a separate search. File applications for each position you would like that you are qualified for.
This is the recommendation of Karen Kelsky (The Professor Is In), for instance, if a department advertises two positions:
But anyway, my answer is yes. If you are a plausible candidate for both searches, apply for both. In most cases the search committees will be made up of different faculty members, and while files may be shared across searches, you can’t assume that they will be. So to make sure your file is read by all concerned parties, send it to both searches.
So you should tailor cover letters and other materials to each position and its requirements. If that means applying for an NTT position that emphasizes teaching and a TT position that emphasizes research, address teaching more in the NTT application and foreground research in the TT position. Let the respective committees behind the ad decide whether they want you.