What you can do is disable the order notification from Shopify backend. Use webhook to know when a order is placed and Use API to tag the order then shoot a mail to Merchant from the API server hope this make sense
Why do you need to tag the Order in the first place?
I understand the purpose of asking questions like this. As a frustrated developer, this isn't really what you want to read as the first sentence of a response you're hoping is going to help you solve your problem. Good to include it, but stating your other comments first, then asking this at the end with a follow up like "If we know what you're trying to accomplish there may be another way to do this" would go over a lot better. To the OP, when asking for help, explaining WHY you need to do a particular thing can go a long way in getting you an answer to your question.
I have this very need which is why I stumbled on this older post. I would like to tag an order that has had a discount applied to it via my script as a way to track orders discounted in a certain way. I would think this would be VERY important to a lot of merchants.
Can we inject hidden form values to the cart page using scripts? Something like cart attributes maybe?