Just keep in mind the NYXL have a different unit tension than the XLs. The calculator they used to have had the ability to choose your string model (XL, NYXL, Pure Nickel, etc), scale length, and gauge. And the one unit tension pdf they still have up is old and doesn't include three NYXLs. But you can use the formula, create a spreadsheet, and approximate the unit tension from that to extrapolate for your set. If I remember correctly, I think NYXL might have a bit higher tension.
But yeah, ¼" is a huge deal for tone and feel. I mean, you turn the screw on a pickup just a little and you've now got a totally different tone, so you go a ¼" out on your scale length, and it's not going to sound or feel the same.
And with Sweetwater's customer service, I love that they're getting you to do the legwork on this. They have god knows how many of this model in stock, but they've got to get a photo from you. Really classy. I stopped dealing with them years ago because my sales rep would just call me to ask if I needed anything. It was obnoxious. And I've read so many accounts of their "55 point inspections," to me they're just the online equivalent of Guitar Center. And I don't know what the hell is up with the reviews on their site; most of those reviews include a review of the sales manager, like that has anything to do with the guitar. It's like some weird cult. It just sits with me wrong. Anyway, I hope they treat you right.