REFPT addresses Reference Points, which are properties of Parts in the geometry.

CRTPT creates Critical Points. Critical Points mark critical points on the ship.

An opening that would cause downflooding if immersed is someting you would want
to mark with a Critical Point. This is the most common use of Critical Points.
When you define one with the CRTPT command it will be regarded as a point of
downflooding unless you tell it otherwise.

Reference Points are used for various purposes. You do not create Reference Points;
they come with the geometry. There is one and only one Reference Point assigned
to each Part. The REFPT command is used to relocate the Reference Point. 
By default Reference Points are located at the origin of the coordinate system (0,0,0). 

Certain tank types make use of the Reference Point. It can be used as a reference
for loading intact tanks.