Given that the design of US doctoral programs is to enable those with a bachelors to succeed, the answer would be, structurally, yes. But for the admission process itself, the effect, while variable, I expect to be weak - with caveats.
There is, in the US, normally some sort of qualifying process before one formally begins dissertation research. Some places and in most (other) fields this takes the form of qualifying examinations; written and/or oral. There are other processes possible, however, probably more likely in engineering.
But there is likely to be some process and the early part of the doctoral curriculum (coursework, lab experience,...) is designed to make passing the bar possible. Usually the early work also guarantees broad knowledge of the field in general before deep specialization for the dissertation. This will also benefit future academics and prepare them for a career. Note that the faculty is pretty certain of the general knowledge of a student who goes through this long process successfully.
For a person with a masters in hand, the qualifying process is probably still in place. I'd expect that having it waived would be rare. This makes it more difficult both for the applicant and for the faculty to judge whether they have the general knowledge or not.
So, a "preference" is probably too strong. But "extra scrutiny" may well be in the minds of the committee members if that is the process for successful admittance.
On the other hand, if a professor has the authority to accept individuals on their own (and probably to give them financial support), the balance may change in the opposite direction. If a professor has need of someone with particular skills in their lab, then someone with a masters might be preferred, being farther along in their education. But the qualifying bar may still be in place, giving the candidate extra tasks, perhaps.
My recommendation is that if you are already in a masters program, then finish it. But if you are not, then there is little if any advantage in starting one if your goal is a doctorate in the US.