Heya,

so as above, the newest SE update (0.6.118) introduced some changes that prevent game-startup when both Warheads and SE are activated.
Rolling back to 0.6.117 on SE fixed the issue but this might be worth looking into if they keep things as is.

Error message was something regarding "item prototype" and what I assume to be the new delivery cannon aiming type they introduced, if needed I can update again and check for the exact phrasing

Is apparently an issue in SE, and will be fixed in SE 0.6.119. (https://github.com/More-Wrong/Factorio-True-Nukes/issues/21).
Please let me know here or on GitHub if it isn't fixed by that update.