@normalized and I are going to agree. 
Prefer human readability.
if not my_var == value:
if my_var != value:
The latter is much clearer.
However, also avoid negatives when you can. For example, when checking for null, prefer:
if my_var:
over
if not my_var == null:
So going back to your original question, I would use better variable naming to avoid using != at all in any form. Personally, I rarely do comparisons like that in reality.
Instead you see things like this:
func _physics_process(delta: float) -> void:
if not is_on_floor():
velocity += get_gravity() * delta
(The alternative would be if is_on_floor() != true or if is_on_floor() == false.)
Or this:
func _on_body_entered(body: Node2D) -> void:
if not body is CharacterBody2D:
return
(There’s actually no way to do this test with !=.)
If you feel strongly about it, contribute to the documentation. The team will either approve it or tell you why it isn’t spelled out. The documentation is maintained by us, the community.
Personally, I think you are focusing on something that doesn’t matter because you haven’t used Godot enough to know that.
To this point, what I tell people on here is if you use the style guide, it’s easier for other people (and future you) to read your code. If, like @soapspangledgames you have another, long-established, style and you’re the only one reading your code it doesn’t matter what you use. But it also makes it easier for you to read other people’s code IMO.
If you follow the style guide then when you come here to ask for help, it’s a lot easier to get an answer. When someone uses PascalCase for variable names and snake_case for constants, it makes it much harder to read their code.