The running order is not the cause of problem. The cause is that, after all these years of IJS, PCS is still not tied to any objective criteria at all.
This is a kind of a paradox: program components are absolutely material, physical factors that can be easily spotted by an eye and are easily compatible. Is a skate gliding smooth or is a skate scratching? This skater is faster than that skater. The edge here is deeper than the edge there. One skater is in sync with music during the whole program, another skater is only in sync during the step sequence. In this body position, it's harder to keep balance, etc. However, at the same time, there is no anchor that could serve as an objective reference point. We have neither the data, i.e., the skater needs to reach X speed during Y section to be 9+; nor we have i.e. an AI generated graphic skating routine that would show how much a skater needs do to be 9+ and to which all skaters could then be compared regardless of when they skate.
So, the judges still re-establish their nines every time comparing the skaters they see on the competition day. No wonder that these nines tend to find a place in the last free skate warm-up group. Although there are also "reputational PCS" (it's another discussion if the reputation is well-deserved or not in case of each individual skater) that skaters would receive regardless of when they skate.
In theory, it is of course possible to set objective, materially-tied references for PCS. In practice however, it would take lots of research, lots of discussion, and overall an enormous amount of incredibly complex work to get such complicated data gathered and sorted. Figure skating is complicated. Is the speed simple? Normally, it is; but the skaters have different speed during different sections of their programs. What should matter then, the medium overall speed or the speed during the fastest section of the program? Edges? Same. And how to measure them, with what technical means? This is before I even mention the interpretation of music. How could this be made compatible? Should it? I can imagine that it may cause more desire to give up the PCS altogether than to develop objective criteria for that.
In fact, the current development could be heading to PCS being abolished or replaced with updated GOE since the programs have a tendency to become more athletic and simpler. But it's just my impression. I may be mistaking.