You're exactly right. This is NO DIFFERENT than if the DEA told the Cannabis Control Commision not to issue retail cannabis license because that would be in violation of federal law. The state used to defend and support it's law regarding the FLRB, even under Deval Patrick's administration. The no longer do that.
It's different because state law explicitly and unambiguously incorporates federal law.
The correct comparison would be if state had a provision that said anyone not allowed to possess marijuana under federal law was not eligible to purchase marijuana under state law. In that situation, the Cannabis Control Commission would be in violation of state law if they issued licenses to sell marijuana.
Right now, any licensing authority that issues an FID or LTC to someone who has received FLRB restoration is violating state law if the person is a fed PP.
I don't know what the solution is here, but I do know state law is clear as day here. The issue is with whether federal law makes you a PP.