There is no interference other then that clearing/unloading the library requires clearing the mex file and unloading the library. The operating system maintains a count of how many times a library is loaded and will not unload it until it is no longer in use.
It is also possible to add mex like functionality to a custom library you will load with loadlibrary. Take a look at extern\examples\shrlib\yprime.c which is a modified copy of the mex yprime example that can be called as a mex file and can be loaded with loadlibrary and has functions that use the mx api.
