This is the problem with relying so heavily on the consistently unreliable projections. They won 89 games, so saying "they should have won 77 games" is pretty ridiculous. The Gnats "should have won 96 games", what should we take from that? The Braves and Phillies are both much younger and are coming off better years, so should Washington start looking to unload everybody and start from scratch?
Remind us how many games those projection systems had the 2018 Braves winning. How about the Athletics? The Gnats? Didn't they have the Astros projected to win the most games? And where are they? Exactly how many of the teams did the projections peg correctly?
The numbers have to be used as a tool - a very good tool, mind you - but still an imperfect tool. You simply can't just go with what the analytics department prescribes 100% of the time in every situation, because they're not infallible. The unexpected happens - Trout has one too many beers the night his brother comes to town, wakes up with a pounding headache, and misses a fastball when everyone KNOWS it's coming in the bottom of the third with two men on.
No one's saying you shouldn't rely heavily on what the analytics tell you - simply that if they're the only thing you use in your decision-making process that you're going to wind up being disappointed more often than you think you will. If AA & Company had approached 2018 strictly as another year in the rebuilding process - as the analytics told them to - there would be one less flag flying over SunTrust Park next April (if those going strictly by the numbers in every situation had been proven right every time, that flag would be flying in Philly or D. C. instead).
You're confusing preseason projections and simply runs scored vs. runs allowed.
It is absolutely true that regardless of the projections or advanced metrics, when you score and give up a certain amount of runs is not a repeatable skill. Over 162 games, run differential is a far more accurate guide for how good you are and how good you will be going forward than wins and losses.
The Braves were as good as their record indicated they were. The Nationals were a better team than their record indicated but still not as good as the Braves. And no, they should not have won 96 games. They should have won about 89-90. The Braves were about where they should have been, if not a win or two below it.
The Mariners should have won 77-78 games based on what they actually did on the field, not based on some projection system. Thinking that team is an 89-win team instead of an 80-or-fewer win team is how executives look stupid down the road and get fired.