In the bypass mode external clock mode, clock is monitored by clock monitor unit (CMU0). CMU used for its operation internal RC oscillator and it basically checks ratio between XOSC and IRC frequencies.
It seems there is no flag allowing to detect whether currently used mode is crystal oscillator or external bypass. Theoretically SW could analyze DCF record content (UTEST Miscellaneous DCF client, bit XOSCEN), what could be difficult, but not impossible. But, is this really needed to detect it SW way as it is application dependent (thus related to specific HW)?