No, you didn't misunderstand, they aren't "EU subsidies". The table is on this page with links to the sources:
en.wikipedia.org
It's true that they are for different years, and it's also quite hard to pin down exactly what "subsidy" there is because of the complex way these things are funded and also that they are unevenly funded from year to year when there are large infrastructure projects with gaps in between them.
But as you say, it shows a tenfold difference between the two countries, so even if either of the numbers had changed in the intervening years, it seems likely that Irish rail journeys receive a higher level of subsidy (per pass-km) than UK ones.
Numbers for subsidy per journey are different from subsidy per passenger-km. Obviously a network with a lot of short journeys made is going to see a lower subsidy "per journey" than one with many more longer journeys, given an overall similar passenger-km subsidy.
There are of course multiple other things that can affect how expensive it is to maintain a network - what speed and frquency does it operate at, what proportion is urban, what proportion relies on complex 100+ years old infrastructure, how much of the infrastructure is at capacity and how much of that is in highly constrained locations, and so on and so on.