Normally the ABS pump doesn't do anything, you can feel when it works under very hard braking.
That bypass of the fluid is normal when driving. Of course fluid is forced through the pump when it's operating. I am not sure however, that fluid under pressure by the pedal cannot get into the pump, just that the least resistance goes around the pump.
Bleeding the typical ABS systems since the 80's is still normal for all but certain unique ABS systems(Teves for example), but there are lots of people reporting soft pedals after bleeding. I have not researched any of those to find out what parts were changed(MC, lines, ABS pump, caliper), or what method they used for bleeding. Some of them are like your example, and normal bleeding ended up with some air in the ABS pump.
Without spending countless hours researching to find out what percentage of those were bled by hard pumping, gentle pumping, vacuum pump, pressure pump etc, its safe to say that normal bleeding has a risk of getting air into the pump.
I simply posted in the beginning that I think a vacuum pump would have the least chance of ending up with air in the pump.
I won a 1995 Crown Vic that I replaced the entire brake system in, and it has a little air in it I'm sure. I swapped in ABS components, it was not an ABS car, but it is now. I installed two rear lines(it's a four channel ABS system), plus MC and the ABS pump etc. I bled it normally, that was back before it was well known that some ABS systems had to have a special tool to get air out of the pump. That car is drivable but the pedal is just a bit softer. I own two 95 Crown Vics, so I know what they should feel like, the other came with ABS.