Upstream has released updates that appear to apply and compile correctly.
This update has not been tested by PaperMC and as with ANY update, please do your own testing
CraftBukkit Changes:
2ed3e3e6e SPIGOT-7210: Fix structures in custom worlds
585ab5ba1 SPIGOT-7207: WorldCreator creates world as super flat even when normal is specified
Messing with game time sent to the client isn't worth the trouble whenever it may be used by the client now and in the future for such a small issue. Mojang, plz fix