I like how it is implemented now, it makes sense. For example you have multiple todo, and you have global checkbox (i call it Master Checkbox). And it marks all as done. 
Though in this current situation i want to have my “Master checkbox” and few additional todo that you have. So first i will mark main todo as “done”, and then step by step will select other ones.
My idea maybe doesn’t make sense for some people, thought i think it would be really usefull. So i think the solution is to make it as option is settings.
The current walk around could be by creating or editing style snippet, for example Obsidian custom checkbox snippet · GitHub
