There is a call to Configure(env) in src/third_party/wiredtiger/SConscript. But there is no cleanup call conf.Finish() in that file.
This is an issue because SCons internally maintains reference to the active configuration object instance and prevents creation of more than single instance at any moment. Thus after execution of src/third_party/wiredtiger/SConscript there is orphaned configuration object instance which prevents any subsequent SConscripts from calling Configure(env).
Actually if one of the subsequent SConscripts will try to execute Configure(env) the build will fail with following message:

scons: ***
File "/path/to/SConscript", line 3, in <module>