The rules I am thinking about involve the interaction of Darkvision, environmental lighting, and the Perception skill:
- Areas of dim light are lightly obscured, and give disadvantage on Wisdom (Perception) checks. [PHB 183]
- Darkvision lets you see in dim light as in bright light, and in darkness as if you were in dim light. [PHB 184-85, and relevant race entries]
- Therefore, anyone using Darkvision to see in the dark should make their Perception rolls with disadvantage (or have -5 to their passive perception)
I don't think this is a hot take, but some people might:
There are really a very limited number of states. The characters can see something without a check. The characters can't see something (because of darkness, range, etc). Or the DM sets a DC and the characters roll against it. In this last case, the characters either have a normal roll, advantage, or disadvantage.
These states are only important if the characters have different vision abilities. That is to say, there could be some cases where some characters may by able to roll while others can't. Or cases where some characters roll with advantage/disadvantage and others don't.
But, in the last three 5e campaigns I have played in, literally everyone has had Darkvision from some source or another. Mostly racial. Sometimes from the Twilight Cleric sharing their ability. Maybe some other source. But it's basically a constant.
The net affect of this is that every player is in exactly the same state: the DM sets a DC, and players roll against it. Functionally, there is little significant difference from everyone rolling at disadvantage, or the DM setting the DC a little higher because he thinks it should be more difficult. Ditto for setting the number for passive perception check. When everyone has the same vision ability, it doesn't really matter if you are strictly following the rules or making everyone roll disadvantage, or if the DM is just adjusting the DC.
Now, there may be some cases where people have different ranges of Darkvision. But that just means someone won't get to roll; it still doesn't matter if everyone within range gets advantage/disadvantage or not. And there may be cases where part of the map is lit differently from another, but that doesn't come up particularly often, and is handled appropriately when it does. And I suppose if someone had the Skulker feat or some other special ability, but as the OP stated, these cases are exceedingly rare.
So, are we always playing "Rules as Written" at my table? One could argue that often we technically aren't. The DM only rarely forces everyone to roll at disadvantage. Does it make any functional difference to the game? Also no. The DM simply sets the DC at what he thinks is appropriate for the level of lighting in a situation, assuming all the characters have Darkvision (which they do). It's a different method with essentially the same result.
Now, I will admit that the math isn't a perfect match. Dis/advantage is normally assumed to be approximately equivalent to +/-4, but this is a rough number. Towards the extremes of a DC range (i.e. a player is very likely or very unlikely to make a roll) the dis/advantage systems has a more notable effect on the probabilities. But I am openly hand-waving that math for the sake of this argument
To go further, I will say this is really the limitation of a system like 5e that has very few modifications to rolls, and bounded accuracy. With a more complex system like 3.x, you could have cases where characters had a lot of highly specific bonuses and penalties that changed due to multiple factors. Not to mention the fact that 3e also had low-light vision and darkvision as mechanically different abilities. But of course, you pay for that complexity with, well, complexity.