It is considered bad form to force brake fluid back from the brake caliper to the master cylinder.
I've read something to this effect before, and I don't understand why this should be so. The compensation port is tiny, so the return of the pistons is slow, but I can't see that anything would be damaged by doing it. But, generally speaking if I am doing owt with the brakes, I'll be flushing through and replacing fluid via the bleed valves.
But I like to get a feel for how easily the pistons move and get a good idea about whether or not the route to the compensation port is clear, so after doing a full clean, flush and bleed, I will generally pump the piston out part way and push them in again to verify that everything is moving and flowing as it should.
Your point about flooding the reservoir is a good one. I only ever did this once on my ST1100ABS. I'd forgotten that I had previously renewed the fluid without needing to replace the pads, so there was too much fluid in the reservoir when I eventually put in new pads. In fact it turned out that there was too much fluid in the system and a couple of days later, when I turned on the ignition, I got warning lights and the customary whirr of the ABS modulator didn't happen. I didn't associate this with my new pads, but the fuse for the ABS modulators had blown - presumably because they were unable to turn. I bled some fluid from the callipers, until the reservoir level was correct, replaced the fuse, held my breath and all was OK again.
I've not made that mistake since !