In my current position, I work within a functional organization. From the lectures I can understand how the disadvantages come about however I have no run into an issue of having silos form between different groups. Every team has their own agenda but when it comes to completing a common task I have not run into any issues. Part of my job is to create engineering change requests which requires collaboration from multiple groups such as supplier quality, manufacturing, regulatory, and R&D. I have never come across an issue where the other functional groups were not willingly to help or non-compliant to the tasks assigned to them in the ECR. This is because divisional leads were always prompt in ensuring these metrics were being met. The one issue I was not too fond of was that functional heads of these tasks were rather removed from the individuals in the trenches of the project and there always seemed to be a knowledge gap in terms of what was being accomplished.
I do enjoy working in this environment, however at one of my previous internships I was based solely on a project based organization. Even though I enjoy the team and environment I work on now, I preferred the project based organization the most. This was because I was able to learn the most from the other members on my team. Working with such a cross functional group provides a gateway of experience into other fields that you normally would not have insight to. There would be a little bit more pressure on say for example the biologist on the team to be the subject matter expert in that field and not have many other resources to fall on. Overall, I preferred this organization structure due to how much I could learn in the younger stages of my career.