if I understand well the question....
You won't be able to RUN a compiled TX map unless all inputs are supplied by the caller (DataPower flow or Message Broker Flow) or available directly to TX (e.g. a local file read, or database query, or queue get, etc.). The map will simply not start and exhibit the error 'source not available' if you pass just one of the two inputs.
So the solution is either:
A) merge both inputs to one: build a single type tree / single input that combine both candidate structures
B) keep two inputs, but populate the unused input with a fake value or explicit "empty" value (as can be specified for an item in a type tree). Yet, given the complexity in passing multiple inputs to a WTX node (requires a collector node), the previous solution is definitely better.
C) variant of A: refactor the two-input global map in 2 single-input / single-output functional maps, that are in turn called by a new "control map" itself taking the variant inputs as opaque payloads wrapped under a suitable header/marker so that the control map can choose the functional map to invoke. The opaque payload is thus only parsed by the functional map when invoked, itself producing variant outputs that can also be returned by the control map as opaque payloads back to the invoker.
My recommendation is solution C.