I thought about making a script that randomly replies a response at a random time in some fixed interval so I wouldn’t have to write this and they don’t find out I’m just automating replies.
Instead of maliciously complying, ask yourself, is your boss crazy, or is he addressing the complaint of a colleague who's claiming that you're not reading his emails (within a reasonable timeframe)?
How do I reason here or provide an explanation?
First, you have to tell us.
Have you been ignoring the requests of that particular colleague? Is that coworker lying? Or possibly being unreasonable?
And if you really don't know what the grievance is, you really need to speak to that person and find out what it is.
What can I do?
Instead of fighting the decision, see if you can come up with an alternative solution that would be just as good to your colleague, and that both your colleague and your boss would be willing to sign off on.
I personally like Asana. It cuts down on the number of back and forth emails. If a task needs to be assigned to me, or if a task is changed, or if I need to approve something, or if the assigner wants to know if I saw it, or started working on it, or what else I'm working on, etc. Asana helps keep track of it all.
Another thing you could do is to ask your colleague to mark his emails to you with a particular abbreviation, to let you know he wants a quick acknowledgment of your receipt.
In the end, I think you'll find that the grievance probably goes deeper than just an email receipt. Maybe that colleague is feeling ignored, or disrespected. Whatever it is, you need to find out what it is and then decide whether you want to do something about it or not.