The shared-neutral thing is called an MWBC. Multi-Wire Branch Circuit.
MWBCs work fine with 2-pole breakers
... in fact they are semi-required! With MWBCs you MUST tie the handles of the two breakers! You cannot have independent throw, or guess what happens: a future maintainer plugs in a radio, cuts breakers until the radio goes silent, and turns off half of the MWBC. Maintainer gets to work taking wires apart, and gets nailed by current on the other half of the MWBC. That's why MWBCs need handle-ties.
In a GFCI/AFCI context, you simply use a 2-pole breaker.
Wait. What? 2-pole AFCIs? Yeah. Really. They exist in every brand. Siemens too.
GE has a special trick. Some GE AFCIs do not require circuit neutral, and that means they are compatible with MWBCs. In fact they are made for that purpose. They still need handle-ties, though.
Siemens has another trick: they make tandem AFCIs (2 AFCIs 1 space) which also do not need circuit neutral (there'd be no room on the breaker for the lug, anyway). This may not fit your needs, but the inner handles on two tandems can be handle-tied to serve a 240V load or MWBC. In fact you can stack several of them, using the inner handles between each breaker for each of a stack of MWBCs. (then the very top and bottom handle are singles). So if you have four MWBCs you have 5 breakers, with 1A not being used for an MWBC, 1B-2A being MWBC 1, 2B-3A being MWBC 2, and so on.
For GFCI, the above "no neutral" technology trick will never work with GFCIs, so you use GFCI receptacles. However if you are using a full-width 2-pole AFCI that may be offered in AFCI+GFCI.
If you did abandon 1 wire in cable, cap it off- never cut
In your application, simply leave the red wire the same length as the other wires, and put an appropriate size wire nut on it and push it into the back of the box. Someday, a future someone may find a use for it - finding things like this in a box when you need it, is pure gold. By the way, you are already doing this on your switch loops, per the "neutral to switch loop" requirement in 404.2(D). Black for always-hot, red for switched-hot and white capped off for future smart-switch use. That became code in 2011.
Honestly most novices should throw their wire cutters in the trash. It's like giving a budding auto mechanic a hammer as their first tool. When you own a wire cutter, all the world looks like a wire that needs cutting! Wires should never be cut. Working in cable you only ever cut the whole cable because you've reached your junction box.
- Wires in boxes should not be cut for snug length - 6" is mandatory and extra is golden, so you have room to recover when a wire end becomes too chewed to put in a wire nut again.
- Wires in panels should not be cut snug either - wires should be long enough to allow hot and neutral to reach every space in the panel (to allow easy rearrangement, and support future possible GFCI).
So byebye wire cutter - I don't even have one in my toolbox, I use my multi-tool for cutting cables (or THHN wires, which is 99% of my work).