You can replace them. I forget the details on how I did it, but I recall doing this for a popular first person star wars game at the time. I replaced the DPMI runtime with a different one and the level load times skyrocketed in speed. My suspicion at the time was that the runtime included switched to real mode to do disk transfers but the other perhaps talked directly to the IDE hard disk staying in protected mode? Not sure, but it was very, very fast with I/O. I was pretty happy with my hack at the time.
My suspicion is you're right. Mostly based on Raymond's blog on the role of DOS in Windows 95[1]. Where people using weird drivers and other things that got in the way of 32bit disk access could massively slow down the system. It's plausible that one extender was being "nice" and using your native drivers or at least trying to be compatible whereas another just went "Nah that crap is slow" and just went for it with a native direct driver and was thus massively faster.
