That is fine, no one way valve... The master needs to suck the fluid back up anyways, otherwise the brakes would never release and eventually you couldn't even push the pedal down (fluid in the calipers aint going no where but back into master...)
Done a little bit of bench bleeding... I had to make my own tool, so for better or worse here was my method, I'll include brake bleeding just cause:
I grabbed a few clear tubes like we used for normal bleeds, and strapped them all together to make less of a mess. I ran lines from the fluid out back into the reservoir.
Like you said when you pump it will pull fluid back in on the out stroke. When you push in try to hold, let the air bubbles start floating up toward the reservoir, then fold/kink/clamp the hoses so that fresh, air free fluid is pulled in from the reservoir. (I wait for the bubbles to rise a bit before clamping so that the tiny bit of fluid that DOES get sucked back into the master from the tubes is hopefully air free.
Once you stop getting air bubbles there, give it a good couple three more goes for the hell of it.
Once satisfied that that is good, re-install on the car and prepare to bleed. I know the vacuum/pressure/speed bleeders are cool, but I have never used ANYTHING better then two, loud, well rehearsed people. While bleeding is simple, it requires good communication to be fast and effect, It is important to be loud and to know what each other is doing.
If your brake system is stock, look up the recommended bleeding order. If changes are made or if you cannot find one start looking at the lines and how they are ran, bleed from the wheel with the longest run of line going to it, and work your way to the shortest.
Have the man on the wheel yell "PUMP"
This is the person in the cockpit's signal to begin slowly and smoothly pumping the brakes 4-5 times. When they begin to do this they should yell "PUMPING"
Once the brakes are pumped up, the person in the cockpit should yell "HOLD" to signify the brakes are under pressure, so the man on the wheel can open the bleeder.
Once the pedal hits the floor, cockpit should yell "FLOOR" while KEEPING THEIR FOOT DOWN, and waiting to be told either to pump again, or that they are "OK TO RELEASE". I typically go three times more then is needed.
Try following that strictly, maintain good communication so you can be sure no mistakes are made... If the problem is not fixed after that, you have bigger issues
