I strongly recommend moving the Projects folder out of the Main branch (or whatever you call it) into the root of the project, at the same level as BuildProcessTemplates and Trunk. In fact, and this is my personal preference, I would keep anything that’s not code outside of a branch. By doing this you only need to take care of the code when merging and branching.
Those who have been working with AX for several years were used to not use version-control systems. MSDyn365FO has taken us to uncharted territory, so it is not uncommon for different teams to work in different ways, depending on their experience and what they’ve found in the path. Each team will need to invest some time to discover what’s better for them regarding code, branching and methodologies. Many times, this will be based on experimentation and trial and error, and with the pace of implementation projects trial and error turns out bad.