One relevant factor here is whether the seniority privileges you describe are unjust. If they are long-standing rules fairly administered, then they may not be. Unlike privileges based on race or gender or religion, such seniority privileges do treat everyone equally over time. Everyone is disadvantaged early in her/his tenure on the job, and everyone has an equal opportunity to be advantaged later on (but what about those who die early?). If the privileges are morally defensible in this way, then gratitude is appropriate when a more senior worker waives a privilege for the benefit of a more junior one.
Now suppose that, for some reason, the seniority system is not morally defensible after all. Even in this case a senior worker may not be morally obliged to waive her/his privileges. After all, s/he is not responsible for the flaws of the system, and s/he is also not a net beneficiary of these flaws (having presumably gone through many years of disadvantage early in her/his tenure). Once again, then, if s/he waives a privilege for the benefit of a more junior worker, gratitude would be an appropriate response.
Gratitude would not be called for (in the way you suggest) only if the system is morally flawed and the more senior person who waives a privilege for a more junior one either has contributed to the design or perpetuation of the flawed system or has been a net beneficiary from its flaws.