Why is the deadline given for refereeing manuscripts so much shorter than the typical time between submission and acceptance?
As an editor, I can say that it is very common for reviewers to submit reviews late, or to ignore invitations without responding so that it takes a while to give up on them and find suitable alternative reviewers. 

This doesn't mean that editors and authors don't notice and grumble about late reviews or notice and appreciate reviewers who submit their reviews on time or early! Please keep submitting your reviews on time if you can and ask for an extension rather than ignoring deadlines if you can't!

In my field, a 2-3 month deadline for reviews is longer than usual (my journal normally asks for a 21-day turn-around, and this seems typical of journals for which I am asked to review). But papers still frequently take a year from submission to publication due to delays in review, revisions, and final publication after acceptance.

However, I would also say that most papers are sent back for revisions if they are not rejected outright, and revisions typically also take months.