In Paris you have the RER lines, which are denoted by letters, and the Paris Metro, which are denoted by numbers.

My question is... are there any Paris Metro stations that are outside of zones 1-3?

Marne-la-Vallée Chessy (the station you'd use for Disneyland Paris) is in zone 5 but the Paris Metro does not go there - just the RER. RER A, to be exact.

Versailles-Chantiers (the station you'd use for Versailles) is in zone 4 but, again, the Paris Metro does not go there - just RER C.

Mairie d'Issy, the southern terminus of line 12, is in zone 2.

Based on my spot checking, it does indeed seem to be the case that all Paris Metro stations are in zones 1-3 but my spot checking isn't comprehensive.

As for why this is relevant... if every destination you're going to be visiting in Paris can be accessed through numbered routes then that means that a Paris Tour travel pass for zones 1-3 would be sufficient vs the more expensive zones 1-5 pass.