It seems that the content is not totally controlled by the channel provider.
I contacted acorn.tv who said that if the subscription were directly through them (instead of through the roku channel) there would definitely be no commercials. They told me to contact roku support.
I tried to contact roku support but it has been over a week and all I get is automatic responses.
It seems that if you have a subscription channel that has program overlap with roku channel free programming (with commercials) the roku channel gives priority to the version with commercials. An undisclosed penalty of subscriptions via the roku channel.