What you are describing is what must be done when one embarks on a project of literary study.

If you just want a story, which is what almost all readers actually read for, just read it as it is, and if doesn't make any sense you are perfectly entitled to think it was a shitty book.

Frankly I think a (fiction) book must always be able to be read as-is, unsupported by outside means, else it is no longer a book.

(You hear that Greg Egan?! You wrote a really bad text book or a pretty good fiction book with pointless homework included every now and then.)