How to rig a model with a rig script that doesnt fit it

One Model is going to be the "master". This is the model you do apply the rig to.
The other is the "Puppet". This is the one that is kept unrigged and the one you render with. Master model naturally kept invisible.

Step one:
Copy paste your model to get a puppet model.

Step Two:

Parent the puppet bones to the master model bones like you would attach clothing to a character.

Step Three: Apply the rig script to the master model. Now both the master and the puppet are messed up together.

Here is where you start fixing the issue.
You make the master model invisible.
You make the master model bones unselectable.

Now you will change the positioning of the bones of the puppet model untill it resembles something cohesive again.

Now the puppet is corrected.

Now you can make the bones of the puppet model unselectable and make the master model bones selectable.

The master model will control the puppet model now.
Congratulations! Now you will be able to bypass rig script oddities whenever they occur.

Important: the bones of the puppet needs to have the lock symbol next to them. Not the master.
You drag the bone from the master onto the corresponding bone of the puppet.