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!