“The more freedom you have as a quarterback, you’ll play better, you’re more confident and good things will happen.” Has Kyle Shanahan been holding back Jimmy Garoppolo this entire time? It’s no secret that Garoppolo’s best stretch of games came in 2017 before he fully grasped Shanahan’s system. Back then, Garoppolo was throwing for 300 yards per game routinely. But the past few years, he became a mistake-prone game manager whom the 49ers didn’t trust to throw often or downfield. That’s why they run so much. But when Garoppolo replaced Trey Lance in the first quarter this past Sunday, Garoppolo…