This is how it works.

When you buy and activate the PS3 version via Mogstation, your account has the FFXIV (PS3) service added to it.

You are required to purchase the PC version and activate that via Mogstation to add the FFXIV (PC) service to your account.

Even if you somehow download the PC version without having the service activated for your account, it will not let you log into the PC version until you've activated the service for your account by actually paying for the PC version.

The plus-side is that this will add a 30-day "Trial Period" to your account. I bought the PC version on top of my PS3 so I could have the convenience of both and have the 60 days.