Unfortunately the manager at the dealer is correct, as Kugas from 2021 onwards were produced without engine covers, most likely as a cost-saving measure. Removing the studs and threads that the engine cover sits on would wipe out any cost saving, which is why your car still has them even though a cover isn't fitted.

Also most modern engines are quite unsightly because they are designed to be hidden by an engine cover, so this is nothing to be concerned about. It also won't affect the operation of your Kuga, other than potentially being fractionally noisier without one. The upside is that as your Kuga has never had an engine cover fitted you won't notice it being any noisier, and if you wanted to you could purchase an engine cover relatively cheaply, especially if you go for a used one.

You may feel a little short-changed by this, but the reality is that all car manufacturers make small unannounced changes to vehicles in order to shave a few pence off the cost of production, it's just that usually they are hard to spot.