Could you explain what you mean by options entry?
You have the ability enable same net check by layer on a per cset basis. In Constraint Manager, open the Same Net Spacing Constraint -> Options worksheet to acces this option.
Are you saying that this can't be changed via skill?
While you can set the SAME_NET property at the net level this takes precedence and enables same net checks for all layers for each net with the property. Normally you will want to set this option in Same Net Spacing csets.This allows for same net checking on same layers but not others.
In Skill to turn on the option for all csets and all layers do (see the Allegro Skill doc for more options):
axlCNSSetSameNet(nil nil 'same_net t)