Is there a programmatic way to check that a journal submission follows a style guideline?
Instead of automating the checks, minimize them by reducing the guidelines! 

The critical pre-submission guidelines are only those where papers that don't follow them would have to be severely edited in a way that will change the referee's opinion about the paper. This is, e.g. a draft that is twice the permitted length, or one where the section organization used is not permitted. Many newer journals are pretty good about things like this (eLife, for instance: https://elifesciences.org/inside-elife/a43f95ca/elife-references-yes-we-take-any-format-no-we-re-not-rekeying)

If I took guidelines 100% seriously, I would be spending a great deal of time not just on margins and formatting (mostly fast once I have a template), but on things like:


Does this journal use Fig., fig., or Figure?
Should subfigure captions be a) or A) or a or A or a or A
Should journal names be abbreviated?
Are the acknowledgments I wrote allowed?
Are footnotes permitted, or is everything an endnote?
Do figure captions have titles?
Is it appropriate to use a comma in an axis label (1000 vs 1,000)?
Is it Eq. 1, Eqn. 1, Eq. (1), ...


Eventually these have to be settled by work from the authors and the editors - but I've found that even different copy editors at the same journal can have different interpretations!

I view rejecting a submission for issues like this as being a waste of everyone's time. With an automated system, it might be less of a waste of time - but I think it also encourages journals to be nitpicky at a stage when it is not important.