Do PhD Committees separate applicants based on whether they are a fresh undergrad or have MS/Work experience? (USA) Does the PhD admit committee look at applicants differently based on the number of years they have invested?
Example:

Set 1: Undergraduates directly applying
Set 2: Master's applicants
Set 3: Undergraduate plus Work Experience

Set 2 and 3 are obviously way more experienced than simple undergrads. So is there any striking differences the committee tries to search for, or are there pre-defined number of seats for the various sets?
Or is all looked at the same? If so, is that really a fair judgement?
If a university were to do that formally, I hope (and suspect) that they would say so. But you can't account for individual preferences in such things. And, I'll also guess that individual bias cancels out in such committees.
Some professors might prefer to admit a student or two who they think might finish early, freeing up resources. Some professors might prefer to have students around for a longer time so that they can get to know them and also have more of an influence on their future.
Work experience might be a plus, but some early research experience is a stronger plus. Work in industry isn't generally a good indicator of success in research, though there are a few exceptions.
But even a student admitted with an MS/MA has to pass qualifying/comprehensive exams, so, in the US, entering with a masters may not bring a big advantage. They also have to choose an advisor with less information since it is sooner. This works well for some, but not all students and professors recognize that in the admission process.
I think that the most important thing, far outweighing all others, is whether the committee can make a fairly accurate projection that admitted students will succeed, both in the degree and thereafter. This is one reason that letters of recommendation have quite a lot of weight in admission decisions and can overcome some deficiencies.
But, for a direct answer, no, there is no strong preference for any of the groups you list.