The main thing I have used loopback for is aligning sub to mains and then verifying the alignment of the mains to each other so I suppose that is option 2 (though the sub/mains aspect has shades of option 1). I wanted to avoid the physical line output as the saffire only has 6 outputs so they're all connected (and my kit is in a rack under the stairs so it's quite inconvenient to have to swap cables physically aka I'm lazy)
I'm uncertain at this point whether this will be necessary in future as I am in the process of moving over to acourate for eq but I can't say I'm remotely au fait with how that works yet hence it would be nice to have something to hold onto that I understand
You can't get a good loopback measurement on the interface without connecting an analog out to an analog in unfortunately. If you ran a digital out to another interface, you'd be getting a loopback on the second interface's output clock, which wouldn't help you with your actual output device. To be clear, the analog output delay on the Saffire is part of what you're trying to measure, unfortunately.
You don't really need the loopback timing reference to get your subs and mains aligned. You can use the "greatest null method" to do that pretty easily, here's how:
1) Invert the polarity of one of your mains or on the sub (but not both). You can do this in JRiver rather than swapping the cables.
2) Then try adjusting your delay on the main or the sub in PEQ (but not both) until you have a 30dB null at the crossover point. You can do this with pink noise/RTA running for greatest convenience, or you can run sweeps in between adjustments. You want this null to be as deep as possible (i.e. tweak the delay until it starts rising again, and then go back).
3) Restore polarity and Voila, perfect phase alignment at the crossover. It works best with stereo subs obviously, but even if you have a single sub, it will get you close. You'll just need to measure with the other main as well and find the best "compromise" delay setting (i.e. a setting between what would be optimal for either speaker). If you're crossing over low enough the wavelengths are long enough you may have more or less the same delay for both.
I don't have a similar easy trick for getting the distance-delay sorted (i.e. getting the mains time-aligned to each other), but the largest source of differential delay in the mains is positional, so you won't go far wrong by just setting their respective distances from the main listening position in the Room correction module. If they're roughly equidistant from the listening position, I'd leave it alone. You can try this with the sub too, set it's physical distance in Room Correction to get it close, and then use the greatest null method to fine tune it.