I have bebop 2 power but I modified the software to fly with all types of batteries.
my rule:
for lipos 4.15 to 3.6 is the ideal - Bebop lowest voltage 3.3353 per cell at 0% and 4.12549 at 100%
for lihv 4.35 to 3.7 is ideal - Bebop lowest voltage 3.3967 per cell at 0% and 4.2937 at 100%
for lion 4.1 to 2.8 is ideal - Bebop not accept official this type of battery
I think parrot stretched too much in the low values, But its look like they do not overcharge
I know people that flyes lipo to 3.30 but he know that battery will last no longer than 1 year.
I will try to find my lipo curve and post it here but in the end of the day you need to choose more fly time or more lifespan for the lipos
and remember charging under 1.5C will also help your battery to last longer
You don't need to reprogram the esc to stop at 3.25 just change this line in the estimator.cfg (under common folder)
[CODE]shutdownVoltage = 9.3; # [V] Will be compared with the estimated no load voltage[/CODE]
Here are the tables from original bebop 1 estimator.cfg the other one in the other folder 
[CODE]batteryPercentageTableVoltage = [ 10.006162,
10.137706,
10.255447,
10.359846,
10.44951,
10.526721,
10.590937,
10.642891,
10.684048,
10.721177,
10.842647,
10.895242,
11.005138,
11.067509,
11.201546,
11.282401,
11.502464,
11.568361,
11.657422,
11.791759,
11.85994,
11.945477,
12.081564,
12.121347,
12.158171,
12.202318,
12.255653,
12.318041,
12.37648];
batteryPercentageTablePercentage = [ 0.0,
0.54,
1.11,
1.72,
2.37,
3.09,
3.9,
4.85,
6.06,
8.14,
17.33,
22.84,
37.54,
43.98,
54.99,
60.49,
73.32,
76.54,
79.83,
84.22,
86.97,
91.42,
96.52,
97.72,
98.42,
98.95,
99.38,
99.74,
100.0];[/CODE]
