Manual:$wgCheckFileExtensions

Details
If true, all uploaded files will have their file extension checked, depending on various configuration settings (see below), to determine whether the upload will be allowed.

If false, most file extension checks will not take place. In this case, almost all file uploads will be allowed.

In version 1.11.1, there appears to be a bug that prevents this setting from actually working. (SpecialUpload.php line 353 isn't checking the value of this variable like it should.) Due to this, it is unclear from the code whether was intended to override. The variable may have the desired effect. This bug was corrected in version 1.13.0.