By pushing the brake pedal down and holding it down, you close the port in the master cylinder that allows fluid to leave/return to the reservoir. If you don't, then you'll get air in the ABS module if the Honda is ABS equipped. Either way, you'll be up for a full bleed if the reservoir empties. You will lose some fluid when you disconnect the caliper but it will be very marginal - just enough to relieve the pressure and whatever dribbles from the hose
You will need to strip back the piston boot to see what's going on. Part of rebuilding a caliper involves sliding the new boot onto the piston then refitting the piston - this allows you to see where you are going.
Usually brake designers stipulate a minimum pad thickness to account for the potential of the piston popping out if both pads on a caliper were to be worn to metal - which for some cars is a real possibility. BMW specifies 3mm as minimum pad thickness but IMO that is a bit generous.
So stepping on the brake pedal with no pads in place and popping out the piston, especially on the front is a real possibility. However it is usually accompanied by a loss of fluid. Try twisting the piston and pushing gently but squarely at the same time.
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