1) how resistance formulas are made for cars, submarines, etc, for equipment operating in a single fluid, not boundary of two of them like boats.
Cars, submarines and other vehicles operating in a single fluid, not at the boundary of two fluid, do not have any wave making resistance. Wave making resistance can be signficicant and even dominant for boats depending on the speed.
2) how prismatic coefficient is defined, it has nothing to do how full the ends are. It is strictly defined by the volume, length and cross sectional area at the largest part.
Correct that the definition of prismatic coefficient does not include anything about how much displacement is in the ends. However prismatic coefficient (Cp) is the ratio of the average cross sectional area to the maximum cross sectional area. (Derivation below) A boat with a higher Cp will tend to have displacement distributed more evenly along the entire length of the boat while a lower Cp will have displacement more concentrated close to the area of maximum cross sectional area. (This assumes a normal distribution of cross sectional area with the cross sectional area staying constant or decreasing with distance from the area of maximum cross sectional area.)
From 1, do you realize a car can have less air resistance at same speed than other car, even if it has larger Cd, if it also has less cross sectional area?
From 2, what happens to maximum cross sectional area when length and displacement volume is kept constant, but Cp is increased?
Yes, it is possible for a car or submarine with larger maximum cross sectional area to have lower resistance.
It is also possible and entirely consistant with the Cp guidance in text books for a boat with larger maximum cross sectional area to have lower resistance at certain speeds than a boat with with smaller cross sectional area. Assuming two boats have the same displacement and length and similar hull shapes, the boat with lower Cp will have a larger maximum cross sectional area than a boat with a higher Cp. If the Cp of the second boat is higher than optimum for the speed being considered te boat with the larger maximum cross sectional area and lower Cp may have lower resistance.
Derivation of Prismatic Coefficient equals Average cross sectional area / maximum cross sectional area
Cp - Prismatic coefficient
Vol - Displacement as volume
LWL - Waterline length
Amax - Maximum cross sectional area
A(x) - Cross sectional area at station x
Aavg - Average cross sectional area
Cp = Vol / (LWL x Amax)
Vol = Integral A(x) over waterline length
Aavg = (Integral A(x) over waterline length) / LWL = Vol/LWL
Aavg / Amax = (Vol/LWL) / Amax = Vol / (LWL x Amax) = Cp