This is a fair point. If the only agency you have is the choice between following marching orders without questions, or unemployment — don't quit.

But I would be surprised if this is the way all EMR software is built. Software development being a creative process, there should always be a feedback loop where managers ask open questions. There lies the agency to recommend spending more time and money, reduce scope in order to guarantee a level you feel comfortable with. You may not get what you bargain for, but it's up to you to decide if it's enough.

Taking the money in return for doing the work is a way of telling your boss you're on the same page. Given your medical context, that may not mean you fully agree, but it evidently means you accepted it.