For coverage, sensor alignment, maybe check if your lightpipe material works with IR. I think remotes are close to visible and therefore likely to work.
Cutting down on the number of remotes is a taller task. One way to go is more integrated devices, i.e. if the preamp and the DAC merge then all input switching is in the same device. If there's just one box then there's just one remote! Modularity makes this viable, but maybe not preferred.
Devices that can learn remotes instead of (or in addition to) the other way around may help with the future product problem.
LEDs can indicate which device is currently being controlled and which buttons are currently active. A screen is only needed when none of the labels on the remote make any sense for a button that needs to be on the remote.
1 Input
2 Output (Process for Syn)
3 Volume up
4 Volume down
5 Mute
6 Gain / Invert / Shape
7 Play
8 Stop
9 Back
10 Forward
That covers everything except the Skoll and the Loki Max, if I'm not mistaken. Which seems sensible, does it not? I did leave out Standby as I cannot envision a use case where you turn your system on or off while remaining in your seat (also I don't think there is any Schiit yet with standby and a remote).
I'd go with four device selection buttons, each assignable by recognizing (or learning when needed) the original remote.
Player, DAC, Preamp, one extra. The four basic player controls as well as the volume controls can stay active while controlling anything but the extra, which may be a secondary player or amp. This feature, controlling multiple devices without explicitly switching what you're controlling, is where you end up with either complexity or limitations. I think this is the part where a clearly good solution is harder to find, the part that may require more thought and discussion. My proposal errs on the side of more limitations, less confusion. Remove the extra that may overlap for a three-device remote where these buttons are always right, only mute and input selection can cause confusion. Duplicate or triplicate all buttons that overlap and maybe a three-device remote that always controls all devices, no device selection buttons needed, isn't a preposterous thought? Maybe exclude muting anything but the amp?
YMMV, but it seems to me that a sensibly complete Schiit remote isn't that much of a beast.