The message specifically said it was due to the “unusually large tip”. They wanted me to confirm that it was intended.

If the article linked below is to be believed, the credit card company does indeed know how much of the transaction is a tip due to the way the transaction is processed. Note that this was at a full-service restaurant, not tipping at the counter for fast food or some other thing.

Consider when you pay with a credit card at a sit-down restaurant, they read the card first. Then you write in the tip on the receipt, meaning that they process this part later after the initial card reading. It is probably different with the tabletop self-checkout devices though.

https://www.quora.com/Why-do-tips-given-in-restaurants-never-show-on-credit-card-statements

I’ve had transactions flagged for (intentionally) leaving large tips before. These large tips were justified for various reasons, such as comped meals.

Could be the specific credit card company I use?

A 50% tip can get your credit card flagged as potentially fraudulent activity.

And tipping culture has creeped in both magnitude (i.e. 15% used to be standard, but now it’s the low end) and scope (e.g. tips prompts at fucking fast food places)

That he is one of the richest men on the planet show that there is no justice, no fairness in the world. Ok, tons of other things too. But this is one of them.