The alter script option gives more information than it should.
Steps to reproduce the problem:
1] Create a model with 2 or 3 tables (model 1)
2] Generate script to create database
3] Create database
4] Add a column to model 1
5] Reverse Engineer from the database to create a new model
6] Compare two models to create the alter script.
The only difference that Toad Data Modeler should show is the addition of the new column but the script has a lot of extra data. It is possible to ignore some of the data but not all of it.
There is no way to make Toad Data Modeler ignore "Filegroup" differences (displayed under Entity).
1] Save the model or put it to Version Manager. Then add a new column to the model.
2] Save the model under a new name, or put it to Version Manager under new version number.
3] Compare the two models (instead of comparing a model with newly reverse engineered model).
Waiting for fix in a future release of Toad Data Modeler.