Li Shenron
Legend
It is near impossible to avoid all ambiguity in natural language without being ridiculously verbose.
Well I would say that even if you get ridiculously verbose, it is still impossible to avoid all ambiguity.
Example with disadvantage:
Player rolls a 1 and a 20. Result is a 1. Player spends luck point and rolls a 5. He can choose 1 or 5.
Example with advantage:
Player rolls a 1 and a 15. Result is a 15. Player spends a luck point and rolls a 10. He can choose 15 or 10.
I was also thinking that this is the way it is supposed to work. There is no reason why someone would choose to spend a luck point before seeing the result of the roll, since Lucky allows you to do so after. If everybody rolls the extra d20 after, then what you say is how things will work with dis(advantage). It is very simple and makes a lot of sense!
As another option... I might be wrong, but I had the feeling that originally Lucky might have granted advantage, but perhaps the designers were aware that a lot of special abilities in the game activate on advantage, and then decided to change it to grant an additional d20 but technically not advantage. As a house rule, it would work also to allow a luck point to ignore the lowest d20 in a disadvantaged roll, but without eliminating the condition of being disadvantaged (as it might prevent some abilities, or activate others).