Let's imagine an Avatar lieutenant and it's Mentor sidekick Strategos says : During the Deployment Phase, you may set aside two Troopers to deploy after your opponent instead of the usual one. Counterintelligence says : Alternatively, this Special Skill counteracts the limit on Command Token use imposed by the Strategic Use of a Command Token, increasing it to two. And Strategic use says : By spending one single Command Token during his Deployment he can: ◼ Set aside one extra Trooper to deploy after their opponent. Does Strategos and Counterintelligence combine to reach 2 trooper in reserve per command token meaning 4 trooper in reserve for 2 command token ?
I'm almost 100% certain the answer is no. The limits you talk about (may set aside one extra trooper, by spending one single command token) are limits on the strategic use of command tokens during the deployment phase, imposed by the default game rules. What CI refers to is the limit on command token use imposed by the strategic use of a command token. The only limit that can be imposed by the strategic use of a command token to "Prevent the adversary from using more than one single Command Token during that first Turn".
Apart from what Spinnaker said... That's referring to the opponent limiting the number of Command Tokens you can use, by their Strategic Use of a Command Token.