I think it depends in part on the brand of jack and plug.

I was in the habit of using RJ45 jacks for everything but I was finding the the RJ11 plugs didn't always seat well. There were also cases of the little gold wires in the jack being damaged - not the wires the RJ11 was actually connecting to but the outer wires being pushed on by the plastic part of the RJ11 plug.

So I would suggest continue to use the RJ45 jacks but either put RJ45 plugs on the phone gear (what I do) or make up little adapters.