Not a lawyer , plenty on here to confirm or reject the following, however, this is how I've heard it explained:
In general, the anti-trust angle applies to a whole market not individual participants. (companies can have different employee rules in the same market). In this case, it's the whole market (NCAA football) vs. a specific entity within the market (SEC football). The SEC or any other conference can have whatever rules it wants under the NCAA framework of members including rules on academic eligibility, transfer, uniforms etc. If the SEC were deemed a market, then rules such as above eligibility could be deemed anti-trust and damaging to the consumers of the market. I think the court argument would be the market percentage test on the SEC side (low % of total market and thus rules are non-impacting) vs the market power test by plantiff (SEC has high market power and is using that power to constrain market)