This response is based on the information provided.  We suggest you discuss with your contracting and finance team, program manager and/or legal department as appropriate.

You are correct.

Those wage determination rates are minimums that are to be paid if contracting with the Federal Government.  They certainly are not ceilings.  We believe there is a typo in the last sentence of your question.  It is certainly expected that a more senior/more experienced craftsman would be paid more than a newly hired craftsman.  Putting it in perspective, next year when a new person is hired into your office at the low end of your GS pay grade, do you expect it is fair for the taxpayer that all in the office get that minimum pay?

These rates are minimums, not maximums.  If they were maximums, people would quit and find a job paying what they were making or better rather than take a pay cut.  We would always be struggling to hire companies with competent workers if all we are willing to pay are minimum wages.

You do not need to justify in the file paying a company's prevailing labor rates.