DC and AC coupling peak-peak difference
An oscilloscope's AC coupling feature removes the DC part of the signal by placing a capacitor in series with the signal.  This is essentially a High Pass Filter.  So some attenuation is expected.

Generic High Pass Filter:



In general, AC coupling is a convenient way to keep the scope trace on the screen when observing small signals "riding" on top of larger signals that are not of interest.  But, as you pointed out, to make an accurate amplitude measurement, DC coupling should be used along with the time it takes to recenter and adjust the oscilloscope's amplitude to make an accurate assessment of the smaller signal.