I don’t have an Arduino IDE to check at the moment. But if I remember correctly, the XTAL frequency is mentioned in the Tools menu where you select and cofigure your board.
Also from memory: The ESP-IDF framework provides a function to estimate the XTAL frequency and the Arduino framework uses it to simplify usage. The default in ESP-IDF however is to set it explicitly.
If you somehow configure the XTAL frequency incorrectly, serial communication will only transmit gibberish. So it’s quite obvious if it’s incorrect and therefore it can’t be the cause of LMIC timing issues.