All this could be quit simple.
An "alarm" that quietly (not silent) would require a pilot to provide an input of any sort every x minutes which could include a "snooze".
If nothing in a minute later it could become progressively louder.
This could not possibly interfere with flight operation even in an emergency or other critical moments when flight crew provides very frequent inputs anyway.
Is it too much to ask that either of two awake pilots at cruise altitude while on auto pilot are asked to do "something" every x minutes?