It's not a "technical side effect" it's what it does. If you don't care about non-repudiation then you don't need to care x.509 certificates in the payment protocol at all.
I'm struggling at trying to figure out your understanding of the payment protocol world. Are you under the impression that CAs would sign payment requests or control private keys? Thats not the case. Only the requester and the requestee will see the payment requests. If x.509 is used its used so that when you receive a payment request signed by a particular party your client (and anyone you show the payment request to) can use their certificate to validate that the request was signed by the right party.
It's a shame my first sentence didn't make any sense, because now I can't edit it. Damn. That's what I get for having 3 hours of sleep and coming in to work early...
I understand what the CA's role is and how the payment protocol works.
I was simply outlining the fact that despite there being a good use-case for this update as well as very small or no technical side-effects, people here are against setting the precedent of implementing code into Bitcoin which necessarily relies on a "trusted" 3rd party, even if that feature is optional.