Actually putting, "I'm not saying the deal is off..." makes me think the deal might be off if I don't 3 & 4. Your other statement, without the qualifier, simply makes me think we need to work on 3 & 4.
The qualifier in this case seems to be an attempt to prime the listener with the fact that this deal is not a sure thing still.
And people are misunderstood all the time. You'll read in to it whatever you want to, but it won't change the way I feel when I say it. It's your job, as the listener, to judge the way I mean it. The simple fact that I have said it doesn't make it one way or the other. Those who are adept at these types of judgements are the ones who move deals forward. Those who cannot get stuck in a cycle misinterpretation that results in a failure to negotiate an agreement.
The qualifier in this case seems to be an attempt to prime the listener with the fact that this deal is not a sure thing still.