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I got an Ibanez AEG8E acoustic guitar and a Focusrite Scarlett 2i4 interface. The guitar has two outputs, a XLR output and a 1/4 inch (6.3 mm) output for instrument cable. The interface provides both inputs.
My question is, which one is better for recording with my interface? Are there any differences in quality or are they interchangeable?
It depends on what features the 1/4 inch supports, but at best it would tie the XLR. Most likely, the XLR is the better option. XLR cables are balanced, which greatly reduces the amount of noise they pick up. 1/4 inch cables can support a TRS mode that uses a balanced signal, but often (most of the time) for guitar cables, they do not.
It is possible in some cases that one type of input on the interface may be particularly better than the other, but most probably XLR is the better option. Another relatively minor side concern, as pointed out by ObscureRobot, is that if phantom power is applied to a 1/4 inch TRS cable, it could result in sending power to the wrong pins. You want to make sure that you turn off phantom power, but as a good precaution, plugging in to the source (your guitar) first before plugging in to the board/interface should prevent a problem even if phantom power was still on.
It looks like your Focusrite audio interface only has a single, global +48V phantom power switch. I assume that when this switch is flipped on, the Focusrite will provide +48V to both of the XLR inputs. I don't know if the TRS jacks are wired to provide phantom power, but my guess is that they are due to the combined XLR+1/4" jacks. If they are, and you use a cable with TRS 1/4" jacks at each end, you could easily nuke your guitar if you plug in a 1/4" TRS cable while phantom power is turned on. Even if you don't, you may one day find yourself with a cable that has XLR on one end, and TRS on the other. If you plug the XLR into the Focusrite and the 1/4" into your guitar, then BAM!, dead guitar.
Assuming that your guitar is wired to safely ignore phantom power if received on its XLR jack, then the safest way is to always use a cable with XLR on both ends.
The reason why phantom power is so dangerous on a 1/4" jack is that the "hot" wire (+48V!) goes to the tip of your 1/4" plug. So when you plug your 1/4" cable in, that hot tip touches the shield contact and then the ring contact before finally resting on the tip contact. If phantom power was turned on when you plugged the cable in, then you probably just fried your guitar's amp.
If you go with 1/4", then just be ABSOLUTELY SURE that the phantom power is OFF when you plug or unplug your guitar!
