Well, for a lot of reasons. First, you can't just "fix" an arm-slot immediately. Arm slots aren't like levers where you just pull it and poof. Biomechanics are deep and to change an arm slot you're tinkering with a lot of things. It's a near impossible change to make at the end of the season - by tweaking on thing, you can create new issues. And the last thing the Cubs wanted is that. And frankly, he wasn't terrible for much of the run - up until his last start of the season he was pitching really well. But that's not kept.
Secondly, Craig Counsell is the manager, he isn't the pitching guy. Tommy Hottavoy and Tyler Zombro are two of the big pitching gurus in the Cubs system. They'd make the changes.
I do think they did change this into the season, though. The Cubs in general have lowered a lot of arm slots - to the benefit of the pitcher. It creates extra run to the arm side and actually is a less violent arm action to aspects of the arm. For Shota, my guess is that they hoped it helped create extra arm side movement on his splitter or to create extra sweep on the sweeper. Sadly, it's also created an issue where the fastball cannot sit as high as you'd want it and he's struggled because of it.