As of the most recent Tinkers Construct version, there is a new modifier known as Rebalanced. Rebalanced serves as a bonus modifier which can give the tool either an extra upgrade, ability, or defense slot. This modifier does not function correctly in the planner, as trying to increment it does nothing. This new modifier also means that tools can now be given defense slots. Because the slot types that show up in the planner are (presumably) hardcoded, it is impossible to see how many defense slots a planned tool has or add creative defense slots to a planned tool.

Potential solutions to the second problem:
Show all slot types, regardless of if the shown type makes sense on the tool
Show a slot type if there is at least 1 of it available (e.g. show the number of defense slots if the planned tool has at least 1)
Add a config option to change which slot types are displayed in the planner