Personally I prefer the Project-Based organization. Being able to be transparent with other departments working on the project would be greatly beneficial. Information would flow more easily between each department versus everyone being on their own and you having to beg procurement or manufacturing for info that you need to do your part in the project, trust me I’ve been there. If one team modifies a spec or tweaks a CAD model and doesn’t inform the other teams/departments then that can have a massive impact on the project that can result in delays or worse. Another benefit is that once the team goes through a few projects together, then everyone starts to get an understanding of everyone strengths and weaknesses and can learn to work around your teams’ limitations.