MATLAB itself does not act to specially protect files or directories, other than the initial setting of read/write/execute permissions at installation time. If a sufficiently authorized user were to set directory or file permissions to allow random users to change files, then MATLAB itself will make no attempt to protect against that.
However, to save resources, MATLAB does not monitor its toolbox directory and sub-directories looking for file changes (to detect changes to files that have already been parsed, to know to re-parse them or to update the user's edit sessions). To tell MATLAB to look inside its toolbox directory for possible file changes, the rehash command must be used. On MS Windows systems, MATLAB installs in directories that are protected by Windows itself, not by MATLAB.
So, on Mac and Linux systems, if you have write access to a directory as far as the operating system is concerned, and also have write access... then MATLAB is not going to stop you from writing to the file. (Depending on which file is involved, it might use a cached version of the file until you tell it to check for updates.)
You are using NFS shared filesystems. It has been several decades since I last used NFS, so I no longer recall clearly how permissions and xattr and access control lists interact across mixed operating systems. Last I recall for NFSv2, if your local system does not allow you access to the appropriate mount point, then you simply cannot talk to the server about a file, but that once you have access through the mount point, that the server has control over access.
But... especially for NFSv2... NFS can simply be unstable, especially with respect to remote files (where the latency adds up or where packets traveling over a backbone are more likely to be lost.) It is not rare for NFSv2 to randomly deny write access to a file. I understand that NFSv3 is more stable that way; I do not have any experience with NFSv4. But back in the NFSv2 days, the truism was that it was a lot more stable and predictable to do all writing to local files and then to copy or rsync the results to the NFS mount point.
