gdkglwindow.c: In function 'gdk_window_set_gl_capability':it might be because you ran configure with the "--enable-debug=yes" option. If this option is absent, it will use the default minimum setting, which is safer than the no setting. Doing this will change some defines related to depreciation that appear to be killing the build at this point - I am guessing this issue emerged as GTK changed since GTKGlExt was released in 2006.
gdkglwindow.c:743:3: error: dereferencing pointer to incomplete type
gdkglwindow.c:749:3: error: dereferencing pointer to incomplete type
To fix it, run the ./configure command as before without the --enable-debug option, then try make again. I hope that works for you.
Maybe someone out there can get the root cause of this fixed one day? *hint hint*