Skyline should be making pretty good use of parallelism at this point. We have spent a lot of time on it. But the parallel functions of Skyline are mostly limited multi-file parallelism, which is controlled by the choice you make a file import time of "Files to import simultaneously" in the "Import Results" form, which has defaulted to "One at a time", but which I just changed to default to "Many", the setting I would definitely recommend on a Dell PowerEdge (at least with the current Skyline-daily, but also with just 2 files). Also, --import-threads=# at the command-line should be even better, or --import-process-count=# for Skyline 19.1 (which has better multi-process performance than multi-threaded).
That said, I am not a huge fan of just building bigger and bigger lists of targets. If the library contains 581,197 precursors, then likely you have used the default of 581,197 precursors for decoys. Though, even with the much smaller Pan Human spectral library from ETH, I felt using 1/4 as many decoys was sufficient and had a performance benefit.
Assuming you have doubled your numbers with decoys, then you would have 1,122,934 precursors, which even with just 6 fragment ions each would mean 6.1 million transitions. If you included precursor transitions extracted from MS1 spectra, then you likely doubled the amount of chromatogram extraction that Skyline does.
For just 2 DIA files on the system you have, this should still work out okay, but the current Skyline implementation would limit you to 2 threads for spectrum retrieval (which would be relatively inactive), 2 threads for chromatogram extractions, and 8 threads for peak scoring. So, it is unlikely to make full use of a Dell Xeon PowerEdge with... how many cores? 24, i.e. 48 logical processors after hyperthreading?
For this, you really need to increase the file count to at least 6. Though, I hope you don't want to increase this many targets to large numbers of biologically important smaples. I would definitely recommend starting with some replicate (more than 2, though) refinement around what you can hope to detect reliably and what you can hope to measure with low enough technical variance to hope to see important biological variance.
Anyway, it should be possible to at least import your two files in parallel, and you should get better performance out of Skyline-daily right now than out of Skyline 19.1. We made some multithreading performance improvements in the past month or so to facilitate new diaPASEF support.
P.S. - Yes, probably your exact scenario would benefit from our allowing higher single-file parallelism at the chromatogram extraction level, given the small number of files and the massive number of transitions and the number of cores on your computer, but we have not yet built that flexibility.