So the question is whether the Commission *and* the Council has exceeded it's competence by agreeing to secret negotiations according to the McCoy agreement. There was obviously an option for the Commission to not agree with secrecy. That secrecy cannot be unconditional, since the Turco case stipulates that "legislative initiatives" and/or "legislative action" have to be transparent.

"The possibility for citizens to find out the considerations underpinning legislative action is a precondition for the effective exercise of their democratic rights."

"[...] such an overriding public interest is constituted by the fact that disclosure of documents containing the advice of an institution’s legal service on legal questions arising when legislative initiatives are being debated increases the transparency and openness of the legislative process and strengthens the democratic right of European citizens to scrutinize the information which has formed the basis of a legislative act[...]"

Is verbatim copypasting of directive articles in a trade agreement a "legislative initiative" and/or a "legislative action"? I'd say yes.