>due to multitasking nature of Linux, the GPIO manipulation is constantly interrupted for short periods when the CPU is doing something else, such as receiving or sending data over network, writing log files, etc.

With a few simple tweaks (isolcpus + irqbalance + setting cpu affinity), you can get rid of the overwhelming majority of interruptions a specific userland program running on a Linux machine could encounter.

If this quote is talking about kernel context switches, choice of I/O scheduler and tick rate in the kernel could be tweaked for better performance.