Bench bleeding is meant to make the job a bit quicker so you don't have to wait for the master to fill through the compensating port. Cracking the line at the master is normal procedure and sometimes you can get away with not even bleeding at the wheels but more so on older cars. I think what happens here is that getting a bit of air into the ABS is causing the pedal to drop in a way that doesn't really feel like it's air but something is bleeding back/around (maybe piston retracting whether it be unwinding or maybe through an orifice) through the ABS and maybe more so if there is a bit of air and more noticed when a person is focused on working on the brakes!
There are some places like the front brake lines just before they got into the hoses where there are going to be high spots and some pretty good flow (high pressure on the pedal) is needed to get the air through which is why I always recommend using 2 people especially for problem cars.