The word affiliate is so loose that it could mean anything. IANAL but I recommend everyone read that word with the tightest of definitions. That means you are not an affiliate if: you are not wpengine, you are not their employee, you are not doing work for wp engine, you are not owned by wpengine, nor do you work for any wpengine companies, and you don't have any ownership in organizations or companies that wpengine also has ownership or control in. And none of wpengine's board of directors or any of the board of directors of any companies wpengine has ownership or control in are your employees or managers.

Effectively, they want to ensure wpengine is not interfacing with wordpress.org through undisclosed ways like shady shell companies. That is the reason for the checkbox.

If you are selling stuff on wpengine or being paid by wpengine for selling stuff on there, you are not an affiliate. you are a seller. if you are selling wpengine subscriptions, you are not an affiliate; just a seller. if you are advertising wpengine services, you are not an affiliate. you are an advertiser.