Modern is always in comparison with older and both are same the difference is only that one is updated version.

In everyday English, that intuition is understandable.

However, Weber is using "modern" as a periodization term, not as a product-upgrade term.

Historians often divide European history into:

Ancient

Medieval

Early Modern

Modern

When Weber says modern capitalism, he means the form of capitalism associated with the modern historical era, as distinguished from earlier forms of commercial activity.

He is not saying capitalism received an "updated version."

So whether Weber's terminology is the best possible terminology is a separate question from what he meant by it.