Allowed emulators:

DS: DeSmume 0.9.11
3DS: Citra (latest nightly)

Please provide proof in the video that you're using that specific emulator: capturing the 'About' window in any emulator works.
Existing runs will be grandfathered in by new runs must follow this rule.

Can we use DeSmuME X432R too?
It's just a build of DeSmume 0.9.11 with higher resolution (x4).

In other ds runs it is also allowed because it is more stable and more accurate like a original ds.

are there any specific settings that need to be avoided to maintain accuracy?

Desmume 0.9.11 with upscalers is fine.

No specific settings afaik are needed.