I've also read that OEMs have their own "version" of tires to their specification, such as softer compound rubber, less tread depth, etc. with the goal being smooth ride, fuel economy, and of course cost. This typically comes up when people talk about short life spans of OEM tires vs. the "same" tire bought from their local tire shop. Not sure on the validity of that notion.
Aside from the tires themselves, I'm guessing a lot of vibration issues after replacement occur due to inconsistencies in installation. The OEM assembly process has a lot of quality control check points where outputs are tested/verified. Your local tire shop is trying to pump out as many installations as possible and don't have (to my knowledge) secondary verifications of the balancing results. It can be a crapshoot based on the experience of the person installing the tires and the level of care they put into their work. Here's some info on what those red and yellow dots on your new tires mean, and where you should expect to see them aligned after installation:
Red/Yellow Dots on Tires (click)