Hey Roy,
If you want to use the integrated RTC you have to put the 32kHz crystal an EXTAL32/XTAL32. This is the only clock source for the RTC.
The Additional Crystal/Oscillator on EXTAL/XTAL is optional but the recommended clock source for the PLL. But you could also use the IRC48 internal oscillator as a clock source for the PLL or use the FLL instead.
The 25 / 50 MHz Crystal/Oscillator is only mandatory if you want to connect a Phy via MII /RMII. It must be the same clock for the Phy and Controller, as they use it for synchronization. If you don’t need the connection to the Phy you could also use different clocks as 8 or 12 MHz.
Take a look at the “Clock Distribution” Chapter in the Reference manual.
Regards