Practically speaking, you have no control over what they think at this point - R1 deadlines are coming up, so you should be focusing on doing the best you can on the applications. Why worry about whether it's a negative or not? What good will that do you? Whether you have a good shot or not is irrelevant at this point -- you're either going to submit for the R1 deadlines or you're not. As for safer schools - that is really up to you whether you feel it's worth it given your professional background to date.
When you're in the midst of putting together applications, the last thing you want to do is play head games with yourself about your chances. That's something to think about in the spring/early summer when you're months before actually putting pen to paper, or after the decisions when you are reflecting back on what happened. Not now.
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