The `registerCapabilities` has no effect on `logging/setLevel`

[vanyauhalin]

Describe the bug

The registerCapabilities has no effect on logging/setLevel.

To Reproduce

import * as server from "@modelcontextprotocol/sdk/server/index.js"

let a = new server.Server({}, {capabilities: {logging: {}}})
console.log(typeof a._requestHandlers.get("logging/setLevel"))

let b = new server.Server()
b.registerCapabilities({logging: {}})
console.log(typeof b._requestHandlers.get("logging/setLevel"))

$ node main.js
function
undefined

Expected behavior

$ node main.js
function
function

Logs

No logs.

Additional context

@modelcontextprotocol/sdk 1.25.3

#882