While it might seem that software runs in an idealized domain free of conventional physics, that's only because operating systems and processors try to provide a "padded cell" in which software can live. But it's a leaky abstraction; for instance, the time it takes to read one byte of memory can vary depending on whether the processor has it on the L1 cache, or has to read it from the DRAM, and even there, it might depend on whether the memory row is open or not, it might get delayed by the DRAM refresh cycle, and so on, and we're not even talking about the case where it's been paged out and the operating system has to read the memory page from the disk. There's a lot of "non-linearities and errant physical effects" there, and as a sibling comment mentioned, the speed of light is still very relevant.

And that's before considering mindfuckery like Spectre and its friends, in which you can, through a careful observation of some timings, watch the effect of an operation which didn't happen, won't happen, can't happen, and sometimes from code which doesn't even exist.