This may not be the correct section but I experienced that some users of the index calculations understand them as 'ready to go' tools. Many of the indeces require adjustment of empirical constants and the pre-set values give disputable results (which is no wonder).
Could this be somehow advised in the tools? Or would it be an option to leave the fields empty so that you are kind of forced to think which parameters are best?
On the other hand, it's not the developers' duty to ensure the reasoned application of the tools. But as more and more questions come up, maybe this could be encouraged within the modules already.
The current documentation is actually sufficient for this but some may not have noticed it yet.