why does the electric potential decrease across the resistor?
The short answer is because electrical potential energy is lost as heat dissipated in the resistor. That, in turn, is due to the work per unit charge required by the battery to overcome the resistance of the resistor and move the charge at a constant rate (constant current). The potential difference $V$ between two points is defined as the work required per unit charge to move the charge between the two points. The increase or decrease in electrical potential between two points of a resistor has nothing to do with the number of charges at each point.
A mechanical analog is a series of objects each of mass $m$ sliding down an incline plane with friction at constant speed.
The objects are analogous to the charges and the sliding at constant speed is analogous to current.
The incline plane with friction is analogous to the resistor.
The decrease in gravitational potential energy due to work by gravity to overcome mechanical friction as the objects slide down the plane is analogous to the decrease in electrical potential energy due to work by the electric field to overcome electrical resistance to move the charges through the resistor.
The heat dissipated in the resistor equal to the loss of electrical potential energy is analogous to the friction heat dissipated on the incline plane equal to the loss of gravitational potential energy.
Hope this helps.