I'm guessing it was something done proactively by TAM in the spirit of the Chilean Supreme Court and Antitrust board conditioning LATAM merger on the merged airline not being allowed to be in the same alliance as AviancaTaca.

Although LATAM has either 12 or 24 months (depending on what I read) to make the single alliance decision, and thus it is entirely OK with Chile for TAM to remain in Star during that period, perhaps LATAM management wants to show that they are going along with the spirit of the ruling right away?

It's far more likely that this is coming from LATAM rather than from AviancaTaca. If it were AV/TA saying "except with our biggest direct competitor" they would be excluding Copa/Copa Colombia rather than TAM. As a central american-hub narrowbody airline with a Colombian component airline, Copa is far more a direct threat to AV/TA than is TAM. But TAM needs to play ball with Chile, at least for the time being.