Jhansenku
In theory, everything you said is correct.
If your source audio is clicks/cues hard panned one way and mono backing hard panned the other, then any stereo channel presented should let you then effectively work with these as 2 mono tracks. No reason why you couldn't (in theory) go multitrack setting on mixer for now, and that sets you up for when you adopt muiltitrack source audio in the future (i.e. one less change to introduce).
For my band, I run stereo backing track, mono drum click (continuous through entire intro and song), and mono band click (just count-ins and any tricky bits mid-song as I want band to listen to the drummer) and Cues. I've also built up a library of recordings of our singer performing most of our songs, and then taken these vocal stems and added them to my multitrack songs so that if she can't make a rehersal, I just enable that track. So, in all I'm using 5 tracks of multitrack from ST3.
The choice to go from stereo source to multitrack is really a time/effort vs benefit/reward decision for you and your band.
The choice to go from using stereo headphone output of an iPad to USB digital, is related to above desire to go multitrack, but also about audio quality (headphone output being worse that digital USB). The audio quality decision really depends on the quality of the PA systems, the style and quality of the audio you are sending, whether you feel there is a noticable/appreciable difference, and whether you feel anyone cares enough. For me that was a no brainer (USB all the way) but I was happy to invest the time in those 1%'ers that might make my band's show that little bit better sounding.
As @Damir mentioned above, one thing to keep in mind when going to USB digital is how far your iPad is from your mixer. There is a lot more latitude for a long cable run of an analog audio cable from your headphone output to a mixer input than with USB.
Generally these are considered USB 2.0 cable runs and the max. distance of the spec is 5m. I'm currently working with this constraint as my band's X32 is used as our IEM mixer with splits for FoH, so I just have to keep me and the iPad within a few metres of our IEM rack, which has been manageable. That said, it has been inconvenient at times so I've just ordered a 10m active repeater USB-A to USB-B cable which I hope will solve this problem. There seems to be a LOT of these types of cables on Amazon/eBay, at a variety of prices, and they are primarily aimed at printers so I expect not all cables will work for audio. @jaytrax had mentioned in a previous thread on this topic (https://support.stagetraxx.com/d/2786-multitrack-to-behringer-xr18/19) the Lindy brand cable, but I've found those tricky to get at a reasonable price in my country (Australia), so I've got another one on order and have my fingers crossed it will work!