The FAQ says I "can enroll as an individual or on behalf of your company" but I didn't find any field where I can indicate that I want to enroll on behalf of my company. How can I do that?
You can sign-up to the app developer programme either as an individual or on behalf of your organisation.
If it's on the behalf of your organisation then you need their authorisation to do so. Essentially, the legal agreement asks you to vouch that you have the authority to sign-up for your organisation and bind them to the legal agreement. There's no box where you have to indicate this, it's all part of the terms and conditions.