I don't believe that there is a clash of themes within X-Sector on account of The Smiler's introduction; in contrast, I feel that the Ministry of Joy ties things together quite nicely. Both The Smiler and Oblivion revolve around themes of experimentation, and we can now assume that both are operated by the Ministry of Joy (though this is never actually confirmed whilst waiting for Oblivion, obviously, as everything is shrouded in mystery). Submission and Enterprise could be explained as earlier experiments aiming to evoke particular reactions (Submission obviously to get potential advocates to follow orders, and the actual dictionary definition of Enterprise "A project or undertaking, typically one that is difficult or requires effort" could link in with the marmalisation process quite nicely if you wanted it too.
Heck, the theme is (within reason) whatever you want to make it, and I link that there's still an aspect of the unknown about X-Sector, but there's certainly no clash of themes.
Whereas in Dark Forest and Forbidden Valley this is a problem, X-Sector feels complete.