When a survival structure places a survival structure block, craftsman NPCs do not seem to register it as a valid work block and ignore it. Torque shafts and similar seem to transfer energy just fine. If the structure block is broken and replaced, the craftsman NPCs will begin to work on the structure block.

Method of reproduction:
Create a structure that has a structure block placed within it.
Scan the structure using the structure scanner tool.
Save the structure with the survival mark checked.
Reload game if needed.
Place test survival structure block.
Place craftsman NPCs and townhall block.
Deposit food into townhall block.
Wait for craftsman NPCs to finish structure.
Craftsman NPCs should ignore the placed survival structure block that was placed by the test survival structure.

Tested using:
Minecraft 1.12.2
Forge 1.12.2-14.23.5.2814
Java 1.8.0_144 64bit
CodeChicken Lib 3.2.2.353
Ancient Warfare 1.12.2-2.7.0.574

Notes:
While this seems a somewhat esoteric problem, the structure within structure method allows structures to be created that not only seem to grow organically, but also allow for structures to be built in a manner not limited to a cubic format.