When submitting a paper to a journal, you don't need to obtain permission to use a book/source reference for literally any single reference you make (like you would in an undergrad essay/assignment)? I accept it might sound a ludicrously simple question, but I am slightly confused as to what 'permissions' entail. My presumption was that you would write a paper, and use footnotes / references like you would any other piece of work (not that you would have to literally email every single author or publisher to say - hey can I use a line on page 23 of this particular book as a reference?)

Please help

You don't need to ask any permission. You only need permission for figures or images. However, in this case you don't ask permission to the author but to publisher of the reference you are using.