Yes, that's what I meant, whether bench bleeding or bleeding the car, you never want to hit bottom, it's hard on the master cylinder because it causes the piston to overtravel it's normal stroke and get into parts of the bore that may not be as polished or could have an extreme taper, which tears at the pistons' seals.
When bleeding the car's brakes, you want to initially pump the pedal rapidly several times, then hold partway down. The person opening the bleeder should open it and close it quickly, long before the pedal travels very far...the idea being you want to have it closed BEFORE the pedal stops dropping....otherwise you'll bottom out, and if you are just sitting there with the pedal on the floor waiting for them to close the bleeder, you are inadvertantly making small movements with the pedal that are sucking small amounts of air back in, as well as smashing the piston against it's overtravel spring and hurting the seals. You want the bleeder opened and closed in a quick 1-2 movement while the pedal is still dropping, not wait until it's down and then close it.
Are you bleeding at all wheels? FWD cars use a split-diagonal brake system, this means one circuit operates the left front and right rear wheel, the other the right front and left rear. You want to bleed in the following order, right rear, left rear, right front, left front. This assures you are bleeding the longest line first, and working back towards the master cylinder. Otherwise, you could just be pushing the same air all over through the system...
If I were you, I'd open the master cylinder lid, and fill to the top. Leave the cap off. Take the rear bleeder screws completely out of the wheel cylinders. Watch the fluid coming from them as it gravity bleeds....and keep the master full of fluid. When they begin draining a solid stream of clean fluid with no air, put the bleeders back in tight, then move to the front and do the same, remove the bleeders, let it flow, keep it topped off, replace the bleeders when you have a good stream of clean fluid without air. Sometimes if there is a large amount of air in there, this will get it moving...air is compressible, unlike fluid, so when you pump on it with the pedal, it just squeezes up and then expands when you release, without moving much. But if you allow for a slow flow, it will work it's way either out to a bleeder or back through the line and out the open MC port (because the pedal is up).
Once you have seen good fluid at all four wheels, and all the bleeders are back in and tight, you should have a pretty good pedal...I'll usually tap each caliper/wheel cylinder lightly with a mallet to dislodge any air bubbles that may be clinging to insde surfaces and make them float to the bleeder, and open one more time, there may be a small bubble or two, or nothing at all, depending. then just for good measure, I'd open the lines slightly at the master cylinder and see if any bubbles escape there....if not, it should be ready to drive now.
I worked alone in a shop at night for 12 years with nobody to help me bleed brakes, and this has always worked...I haven't left on on the rack yet for lack of brakes...
If you just simply can't get a good pedal, just take that MC back to Advance...they'll defect it out and give you another, just tell them you bled it correctly but it won't build pedal height...and start over, doing it like I said, install it first, leave the lines off, and put the bench bleed tubes on it, then bleed it with the pedal, taking care not to bottom, and feeling what the air feels like as it purges and also being able to feel the pedal stroke firm up so you know it's happening. Then put the lines on, and assuming you already did the gravity bleed at the wheels, you should have all hella brake pedal now...
Yes the pedal feels different with the car running, the booster's assist negates the little bit of pedal you have, making it hit the floor and feel like there's nothing there.....I don't bleed with the motor running...like I said, the harder you push air in a hydraulic system, the more it wants to just compress rather than move....
An old trick to tell if you still had air in the system was to rapidly pump the pedal several times, then hold, and have someone watch the resevoir when you release the pedal abruptly...doing that compresses any air very tightly, and when you release the pedal, the compressed air rebounds back to original uncompressed volume so violently, it shoots a large forceful shot of fluid back through the return port into the resevoir....instead of the gentle rippling disturbance you see when fluid returns under normal fluid pressures...but the design of the Honda's MC makes this difficult to see...