I'm getting a bunch of this warning coming up and it makes it really annoying to spot any actual issues. I've tried changing the anchors and using set_deffered but neither seem to make a difference.
W 0:00:06:754 _set_size: Nodes with non-equal opposite anchors will have their size overridden after _ready().
If you want to set size, change the anchors or consider using set_deferred().
<C++ Source> scene/gui/control.cpp:1443 @ _set_size()
This is the function that seems to be causing it, it's called from set_text and just resizes a custom tooltip based on the actual size of the text.
func resize() -> void:
label.custom_minimum_size = Vector2(label.get_content_width(), label.get_content_height())
label.size = label.custom_minimum_size
margin_container.custom_minimum_size = label.size + Vector2(10,10)
margin_container.size = margin_container.custom_minimum_size
custom_minimum_size.x = label.size.x + 18
set_deferred("size", custom_minimum_size)
label.text = "[center]" + label.text + "[/center]"