The first of these is specific to how User Functions are inserted into the GUI. Normally, you would put the function name assuming that MATLAB would resolve it in the PATH. However, Compiled MATLAB does not have a concept of a MATLAB path so all references to external User Functions should refer to them using their full paths to the file (usrFcn -> C:\Documents...\usrFcn.m). Furthermore, MATLAB is unable to call other local functions called by a User Function as one would expect due to the aforementioned lack of a mutable MATLAB pathPATH.
Arbitrary Line Scanning
Since Compiled MATLAB does not support importing .m files out of the box, adding your own custom arbitrary line scan shape is no longer possible.