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For one, if you limit your definition of freedom to "freedom to do things" and disregard "freedom from things", you end up being pro-organized-power, which is essentially pro-business.

What do you mean the companies making the rules? Do you mean laws or rules like "you have to check your email after 5 pm"?

You've framed the issue in a way that I think obscures a straightforward application of core libertarian principles.

Companies are just associations of people bound by various contracts, all freely entered into into.

So the libertarian belief in freedom of association and freedom of contract lead naturally to the support of any voluntarily formed organization including companies of all types, churches, non-profits, little leagues, partnerships, activist groups, and so on.