Well, colour me surprised. I was planning on doing a very basic upgrade, thinking I'd have to manually copy all of my settings back.
I was wrong.
The only thing I can assume is that when running a backup via iTunes, the Cydia app settings somehow manage to weasel their way into the area of the file structure that get backed up. It was bare bones to start, but as soon as Springtomize was on there, all my icons arranged themselves as they were and had all the other config options (no labels, 5x5, concave row of icons along the bottom) as well as Auxo (option to switch music/toggle controls, customised toggle options). Even the regular iOS applications managed to maintain their settings (which I was NOT expecting, although I'd hazard a guess it's been like that for a while, I've just never known). Really happy with how easy it is.
And I'm glad I've gone the route of installing individual Cydia packages as well. Feels like I have more control than just using PkgBackup and expecting everything to work (especially with compatibility issues that I had honestly not expected).