The software is being written for the customer and/or management, and they're paying for it. They have a legitimate right to know why the estimate is what it is, and to understand what work is going to be done. If they want to exclude parts of it because they don't see the value, then that's up to them because they get what they pay for.
If you can't explain why it's a bad idea to cut certain parts out, or why certain things take the time that they do, then it's a failure on your part as the engineer, and not theirs.