Ravenna is correct you need the Green ghost gauge effect for all this to work, also here is something else that may help.
The first document kinda explains landing gear scrape points and waterplanes and the values to change. The second is the VN PT Boat CFG file with the changed values so you can start on the water. Note the depth charge effect used with Green ghost gauge. Not sure where this came from so some credit is due to somebody.
e.g. A6M2
[contact_points]
//0 Class
//1 Longitudinal Position (feet)
//2 Lateral Position (feet)
//3 Vertical Position (feet)
//4 Impact Damage Threshold (Feet Per Minute)
//5 Brake Map (0=None, 1=Left, 2=Right)
//6 Wheel Radius (feet)
//7 Steer Angle (degrees)
//8 Static Compression (feet) (0 if rigid)
//9 Max/Static Compression Ratio
//10 Damping Ratio (0=Undamped, 1=Critically Damped)
//11 Extension Time (seconds)
//12 Retraction Time (seconds)
//13 Sound Type
//14 Airspeed limit for retraction (KIAS)
//15 Airspeed that gear gets damage at (KIAS)
point.0=1, -20.21, 0.00, -1.45, 3200, 0, 0.10,180.0, 0.40, 2.5, 0.80, 7.5, 5.00, 0, 0, 135 // ,,-1.55,75.0
point.1=1, 1.71, -5.76, -6.60, 2200, 1, 1.05, 0.0, 0.50, 2.5, 0.83, 2.5, 4.00, 2, 0, 135 // old1.41,,-6.60
point.2=1, 1.71, 5.76, -6.60, 2200, 2, 1.05, 0.0, 0.50, 2.5, 0.83, 2.5, 8.25, 3, 0, 135 // old1.41,,-6.60
point.3=2, 0.00,-20.00, 0.25, 3200, 0, 0.00, 0.0, 0.00, 0.0, 0.00, 0.0, 0.0, 5
point.4=2, 0.00, 20.00, 0.25, 3200, 0, 0.00, 0.0, 0.00, 0.0, 0.00, 0.0, 0.0, 6
point.5=2, -10.25, 0.00, -3.00, 3400, 0, 0.00, 0.0, 0.00, 0.0, 0.00, 0.0, 0.0, 9
point.6=2, 6.41, 0.00, -4.08, 3200, 0, 0.00, 0.0, 0.00, 0.0, 0.00, 0.0, 0.0, 4
In CFS2 you have to choose between having a seaplane as a true amphib (with land AND water capability) or a true floatplane (water capable only). There's no having the ability to water-start a land/water amphib model with gear if you want it to start in water first at mission loading. As you've discovered, starting an amphib in water will always load with 'gear-down' first and sink. A floatplane, on the other hand, WILL water-start, but it must not have any active landing gear.
So what you want to do is disable the gear on the amphib to prevent 'gear-down' and subsequent sinking, thus making CFS2 regard it as a floater only. I know, it sucks, but everything has a limitation, right?
To change an amphib to a floater for water-starting, start with the cfg file. Put backslashes in front of the landing gear entries in the Contact Points section to comment them out and disable them, like below (they are always listed as point.X= 1):
[contact_points]
//point.0= 1, 16.083, 0.000, -8.758, 3200, 0, 0.693, 41.600, 0.100, 2.500, 0.700, 5.000, 5.000, 0
//point.1= 1, -2.917, -7.000, -8.700, 2200, 1, 0.693, 0.000, 0.206, 2.500, 0.881, 5.000, 5.000, 2
//point.2= 1, -2.917, 7.000, -8.700, 2200, 2, 0.693, 0.000, 0.206, 2.500, 0.881, 5.000, 5.000, 3
point.3= 4, 16.083, 0.000, -4.567, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 2
point.4= 4, 12.083, -2.100, -4.967, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 3
point.5= 4, 12.083, 2.100, -4.967, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 3
point.6= 4, -16.083, -2.100, -3.767, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 3
point.7= 4, -16.083, 2.100, -3.767, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 3
point.8= 4, -3.920, -42.000, -3.167, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 2
point.9= 4, -3.920, 42.000, -3.167, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 3
point.10= 4, -1.920, -42.000, -3.167, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 2
point.11= 4, -1.920, 42.000, -3.167, 3200, 0, 0.693, 0.000, 0.206, 2.500, 0.781, 0.000, 0.000, 3
point.12= 2, 1.267, -42.000, 8.000, 10575, 0, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 5
point.13= 2, 1.267, 42.000, 8.000, 10575, 0, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 6
point.14= 2, -21.583, 0.000, 2.500, 10575, 0, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 9
point.15= 2, 8.833, 0.000, 2.500, 10575, 0, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 4
"Point.X= 4" is float points for water and "= 2" is scrape points for use in crashlanding.
Leave the *.air file as is, in case you want to re-enable the gear again later in the cfg.
Hope this helps
[fltsim.0]
title=VN_PT_boat
sim=VN_PT_boat
model=
panel=
sound=
texture=
kb_checklists=
[contact_points]
point.0=4, 6.499, -5.250, -1.409, 1600.000, 0.000, 0.000, 0.000, 0.850, 2.500, 0.650, 0.000, 0.000, 0.000, 0.000, 0.000
point.1=4, 6.498, 5.250, -1.409, 1600.000, 0.000, 0.000, 0.000, 0.850, 2.500, 0.650, 0.000, 0.000, 1.000, 0.000, 0.000
point.2=4, -12.745, -4.759, -1.211, 1600.000, 0.000, 0.000, 20.000, 0.950, 2.500, 0.650, 0.000, 0.000, 2.000, 0.000, 0.000
point.3=4, -12.692, 4.540, -1.263, 1600.000, 0.000, 0.000, 20.000, 0.950, 2.500, 0.650, 0.000, 0.000, 3.000, 0.000, 0.000
//point.4= 2.000, -14.086, 0.000, 1.641, 1800.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 9.000, 0.000, 0.000
//point.5= 2.000, 8.563, 0.000, 1.059, 1800.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 4.000, 0.000, 0.000
//point.6 = 5.000, -13.014, -2.410, -2.415, 1600.000, 0.000, 0.000, 50.000, 0.000, 0.000, 1.000, 1.000, 1.200, 0.000, 0.000, 0.000
//point.7 = 5.000, -13.071, 2.410, -2.433, 1600.000, 0.000, 0.000, 50.000, 0.000, 0.000, 1.000, 1.100, 1.500, 0.000, 0.000, 0.000
static_pitch=-3.999023
static_cg_height=5.584627
[Views]
eyepoint=5.111210,-2.986815,11.340420
[LIGHTS]
panel=0, 0, -105.00, fx_dpthchrg
//[LIGHTS]
//panel=10.3, -1.22, -60.80, fx_tpdexpl_l