Back when I applied to college many years ago, IIRC all the colleges I applied to used Common App as mentioned in a sibling comment (I only applied to five top universities, no idea about the less competitive ones which constitute the majority), but each one had a distinct set of extra questions and/or short-form essays, and no amount of software could save you time on those. I even had to carefully customize the “common” personal statement in order to play to each recipient’s (perceived) interests.
I guess cookie cutter bulk applications could be used for fallback options, but those are not the time consuming ones in the first place.
The consequences of this is now it is truly much easier to apply to a bunch of schools for undergrad.
Note, this is not the same for grad schools. I have been applying to graduate schools, and they seem to have their own systems (but there seems to be a common platform called "Applyweb").
The only thing the common app does is standardize the name/dob/address form that's two pages of paper anyway. The essays, which are by far most of the work, are mostly different. Oh, and the schools all still charge full application fees.
As for paying the application fee, it's not too hard to get a waiver. All you have to do is get your guidance counselor to sign off on a waiver form. (That is actually not just for the Common App either: nearly every school will accept that sort of affirmation of need and waive the fee)
The primary reason fees exist is to make them high enough that students who aren't all that interested in attending don't bother to apply. Believe it or not, for most schools the application fee really doesn't impact their budget much. Take a mid-size school with 20,000 students and a freshman class of 3,000. They might get 12,000 applications that progress far enough that the student submits a fee. Take away 3,000 for fee waivers, and average a $60 fee, and it adds up to $540,000. Seems like a fair bit of money, Given a staff 20, marketing budget, etc., it's a very minor consideration.
Sure, it's not nothing, but having lots of not-very-interested applicants makes it extremely hard to make a target enrollment goal because you end up accepting so many students that won't attend. So you either come under your goal because you accepted uninterested students, or you accept too many to make up for it, making it look like your less competitive at the same time you risk enrolling more students that the school can handle on such short notice (I've seen that happen, it's not good for the school or the students).
Source: I work in higher ed analytics.