The webservice file upload script (webservice/upload.php) takes the $CFG->maxbytes setting and applies it to the total size of all files in any of the users draft areas plus the uploaded files. This is to prevent the webservice being used to completely fill the disk of the Moodle server.
An upload with filepicker/filemanager applies the maxbytes setting to each file in the upload (so a limit of 20MB allows 4 15MB files).
This could be split into a separate setting or the filepicker/filemanager could be changed to use the same logic as the webservice upload (it is hard to implement the filemanager/filepicker logic in the webservice without big API changes).
Note: This only applies if
MDL-22236 is integrated without further changes.