Yes. correct. Issue confirmed.
It happens with ESP32 and ESP32-S2 only.
Other SoC activate UART using UART_SCLK_XTAL clock source are safe.

Fix on the way.

@deltecent - Please test the PR #10642 and let me know.

@SuGlider I am very new to the Arduino IDE environment. Is there documentation on how to test a PR?

@deltecent - In order to test a PR, it is necessary to create an Arduino boards from a sketchbook.
It is documented here: https://docs.espressif.com/projects/arduino-esp32/en/latest/installing.html#macos
In a few words, the whole process shall go like this:

1. create a hardware/espressif/ folder under your Arduino Sketchbook folder (usually ~/Documents/Arduino)
2. clone ESP32 Arduino into this folder
3. go to <cloned_arduino_folder>/tools and execute get.py to install all the tools and libraries
4. restart your Arduino IDE and go to Menu->Board option to see the ESP32 Arduino (in sketchbook) new board.
5. go to the <cloned_arduino_folder> and execute git fetch origin pull/PR_NUMBER/head:PR_BRANCH_NAME using PR_NUMBER as 10643 and BRANCH_NAME as any name you prefer.
6. in to the <cloned_arduino_folder> execute git checkout PR_BRANCH_NAME using the selected branch name from (5)
7. go to your Arduino IDE and build/upload again the testing sketch

@SuGlider Thank you for those instructions. They worked great. PR #10642 appears to have fixed this problem.

I want to point out that the comment for this PR in the test program above is in the wrong place. The PR corrects Serial.updateBaudRate():

void setup() {
  // put your setup code here, to run once:
  Serial.begin(115200);
  delay(500);
  
  Serial1.begin(230400);
  Serial.printf("%d\n", Serial1.baudRate());
  // Clock is UART_SCLK_REF_TICK as expected

  Serial1.updateBaudRate(460800);
  Serial.printf("%d\n", Serial1.baudRate());
  // Clock is still UART_SCLK_REF_TICK, should be UART_CLK_APB <<---- FIXED by the PR

  Serial1.end();
  Serial1.begin(460800);
  Serial.printf("%d\n", Serial1.baudRate());
  // Clock is now UART_SCLK_APB as expected
}

void loop() {
}

Thank you for the quick fix!