Code Veronica was counted as a side story, simple as that.

It doesn't cover the end of Umbrella, it covers the end of two Umbrella bases, the one in South America and the one in the Antarctic.

You've forgotten about Oswald Spencer, the head and leader of Umbrella, Alfred and Alexia were not the heads of the company.

Really, RE4 shouldn't be RE4 since it has nothing to do with zombies or Umbrella or whatever, but then Resident Evil : Leon Does Spain doesn't really fit well as a dramatic name, does it?