distance between player and designer

There is a problem that I haven't seen solved yet, and I don't even know if it's solvable:

There is a disconnect between what the player intends to do when choosing an option (horizon of intention) and what the designer has defined will happen when choosing the option (horizon of action).

This disconnect can be minor if there is a strong enough sense of construction and the designer knows with certainty what the player intends to do when choosing an option.

But it can also not be, and the player may have an intention that is opposed to what the designer thinks.

Many games use 'flags' to solve this:

SHOPKEEPER: Here's your bag sir.
 * Thanks for your service (sincere)
 * Thanks for your service (ironic)

In my opinion, these types of solutions are sub-par.

I don't think it's a good option to take the player out of immersion with these flags.

But at the same time, the risk of falling into a very large gap between intention and outcome is very high, and generally generates more rejection than a simple flag.

What do you think? Have you seen this problem solved in a different way?