Most definitely. You need to resolve all your end of phase abilities before you can check for control and then award
VP.
Rules Commentary wrote:Control (objective marker): A player controls an objective marker at the end of any phase or turn in which their Level of Control over it is greater than their opponent’s. At the end of a turn, control of objective markers is determined before any Victory points are scored. See Level of Control.
Rules Used at the End of the Command Phase: While most rules used in the Command phase have to be used in the Command step of that phase, if a rule explicitly specifies that it takes effect at the end of the Command phase, then that rule takes effect at the end of the Battle-shock step of the phase, instead of in the Command step.