It is not possible to build WebKit under Windows if WebKit is checked out via git. Regressed at r65143 https://bugs.webkit.org/show_bug.cgi?id=41982 It would be better to compare $(WEBKITLIBRARIESDIR) and ..\..\..\WebKitLibraries\win\tools instead of check the .svn directory.
r65143 was rolled out in r67482, so this bug should no longer occur.