The conflict is in your reasoning. Cruz dinged Trump for getting involved in a state issue, and choosing sides. There is no way to stretch that to mean Cruz supported keeping the flag, it’s just another cheap shot at Cruz based on nothing logical.
I'm not buying your reason why the ad was made. The obvious purpose of the ad was to portray Trump as anti-flag and appeal to the confederate flag supporters that Ted stands with them. If Cruz supported the removal of the flag, why make the ad? Unless he is using the issue as a way to garner votes (pandering). And if he is upset that Trump "got involved" in a state issue by expressing his opinion as a private citizen, he is not that good of a constitutionalist.