Seems to me that by setting the fine at $2.5M the commissioner is invoking this provision which specifically states that this situation is not covered in the Constitution and By-laws.
Otherwise, the fine would be capped at $1M as stated by the provisions you posted in #31.
Nah—they’re just interpreting it as an additional circumstance—say, the players having threatened a boycott—that gives them the flexibility to up the fine.