Both Passmark and Geekbench are aggregates of a variety of tasks. If you dig into the individual tests that constitute this aggregate score, you will find different platforms perform better, or worse, on certain tests than others. I would wager that, for many applications, only a subset of these tasks are relevant to the performance of the application, yet such benchmark suites distil out all nuance into a single value.
Here is a personal anecdote. I have tried running CASTEP (built from source), a density functional theory calculator, on both an M1 Max MacBook Pro [0], and on a Ryzen 7840HS Lenovo laptop [1]. A cursory glance at those Geekbench results linked might make you expect that the performance is roughly equivalent, but the Ryzen outperforms the Mac by about 4x, a huge difference.
What happens if we try and dig into any particular benchmark to explain this? If you click on any particular benchmark in the Geekbench search lists, you will see they test things like "File Compression", "HTML5 Browser", "Clang". Which of these maps most closely to the sorts of instructions used in CASTEP? Your guess is as good as mine.
If anything, I would say Passmark is quite a bit less abstract about this. Looking at the Mac [2] and Ryzen [3] Passmark results, you can see the Ryzen outperforms the Mac by about 2x on "extended instructions", which appear to involve some matrix math, and also about 2x on "integer math". The Mac, meanwhile, appears to be extremely good at finding prime numbers, at over 3x the speed of the Ryzen. Presumably the Ryzen's balance of instruction performance is more useful for DFT calculations than the Mac's, which perhaps is weaker in areas that might matter for this application, but stronger in areas that might matter for others.
Of course, optimization is likely a component of this. How much effort is put into the OpenBLAS, MPI, etc, implementations on aarch64 darwin vs. x86-64 linux? This is a good question. It is, however, mostly irrelevant to the end consumer, who wishes to consume this software for use in their further research, rather than dig into high-performance computing library optimization.
[0] https://browser.geekbench.com/search?q=7840hs
[1] https://browser.geekbench.com/search?q=m1+max
[2] https://www.cpubenchmark.net/cpu.php?cpu=Apple+M1+Max+10+Cor...
[3] https://www.cpubenchmark.net/cpu.php?cpu=AMD+Ryzen+7+PRO+784...