Those are 2 different binaries and thus should have different
.so names. Just use the $PYTHON_SO for that to happen.
https://bugzilla.gnome.org/show_bug.cgi?id=738157
$(PYTHON_INCLUDES)
libgstpythonplugin_la_SOURCES = gstpythonplugin.c
-libgstpythonplugin_la_LDFLAGS = -avoid-version
+libgstpythonplugin_la_LDFLAGS = -avoid-version -shrext $(PYTHON_SO)
libgstpythonplugin_la_LIBADD = $(PYTHON_LIBS) $(PYGOBJECT_LIBS) $(GST_LIBS)
libgstpythonplugin_la_CFLAGS = $(GST_CFLAGS) $(PYGOBJECT_CFLAGS) $(GST_PLUGINS_BASE_CFLAGS) $(PYTHON_INCLUDES)