That's actually a good point, setting precedent by one side not being represented properly.
Thinking further, one company could easily setup another and sue it for one thing or another. The set-up company presents a believable but purposefully flawed case and voilà: legal precedent.
Some have made the argument that certain government agencies are participating in this sort of sham arrangement, under the guise of 'consent decrees' where an interest group sues an agency, and 'forces' the agency to assume a new (or expanded) power. This is a contentious issue (as you might have imagined).
This could happen in our current system. For example, if the DoJ in Apple had a side agreement that Apple would lose the encryption case. Obviously that's not what happened, but your conspiracy scenario isn't any more likely if courts forced a case to continue.
