There is no reason this couldn't be applied to the bonus rather than the score.
The score gives you more granularity to work with. You can have, say, an average deadly poison giving you 2d6 "fatality points," which, if they equal your CON, you die. Heroes like PC's will probably be able to survive these venoms, common people probably can't. You could have a weaker poison dealing 2d4 "fatality points." Rolling dice is fun, tracking individual numbers not so much, so it throws better than "1 fatality point" or "3 fatality points."
If it's like 3E with a 0 average, you are right. But of course, they have implied 0 will be the minimum and there will only be bonuses, in which case this would also work without using the scores.
Again, the bigger number (the score) gives you more granularity. This means you can have cascading effects, broader continuum, and more breathing room in general. Add this to the fact that "18 Strength" is a very classic D&Dism that the game would probably be breaking brand recognition if they ditched, and you've got a better reason to keep them than to ditch them.
This would also work without scores. Roll D20 + your bonus to beat 10 + their bonus.
Right, but that's more math and more formulae and more blaaaaaaaaaaaaaaaaaah. It's a lot easier and less wordy to say "d20 + bonus vs. SCORE," and it has the advantage of working just like AC and other defenses -- a static number that is noted on your character sheet.
This one is the closest to needing scores, but again if they are moving away from penalties (ie, all stat mods are bonuses and 0 is the minimum instead of the average), you can still make this work without scores easily enough (eg, for every 2 you make your roll by you get a point, succeed when points > opposing Wis bonus).
Why would you want to make it work without scores when it works just fine with scores? In fact, it works slightly better -- more granularity, pre-made existence on the 1-20 continuum, equivalence to defenses in the game....why change it to a somewhat counter-intuitive "bonuses are also scores sometimes" kind of system?
Again, the only reason bonuses would not be interchangeable with the score is if they went back to 1E where the bonuses weren't even (ie, not +1 per 2 points of score). In that game it was like 15-16 was +1, 17 was +2, 18 was +3 or similar. Because it wasn't a standardized progression across the range of the score, the bonuses were not functionally identical to score.
As of 3E, bonuses and scores are the same thing expressed in two different ways. The score is redundant.
They were so busy thinking about whether or not they
could, they didn't stop to think about whether or not they
should!
A relationship does not imply equivalence, or redundancy. There are many uses for a 1-20 score in a d20 game aside from deriving a bonus. That is one of the purposes. There are others (serving as "condition hit points," "situational defenses," "check DC's," etc.). Bonuses can be made to work that way, but if we're going to say "10 + bonus," why not just call that a "score" and note it on your character sheet with the rest of your scores?