How can the equation of dropping and bouncing a ball have a y intercept if the ball cannot be dropped from 0 cm?

You can define the height of zero to be at any level you want.
Then the equation will give the height of the ball above that level
at any time.  If you define zero height as the position of your hand
just as you drop the ball, then the equation will give negative values
for any time after the drop.  If you define zero height as the floor, then
the equation will give a value of zero at the instant of every bounce,
and positive values at any other time.

For a graph of (something vs. time), the x-axis is usually time, so the
y-intercept is the height of the ball at the drop, when time begins.
That's just the height from which it's dropped ... relative to whatever
height you decide to define as zero.