It looks like a library bug. rtc.set_time constrains the year to the range [00-99], but then calls the corresponding RV3028 driver routine, which treats it as a 16-bit unsigned int and subtracts 2000 from it.
When you take all that into account, the results you got are actually inevitable:
00 (rtc) → -2000 (RV3028) → 0xf830 (16-bit uint) → 72 (BCD) → 48 (decimal)
21 (rtc) → -1979 (RV3028) → 0xf845 (16-bit uint) → 105 (BCD) → 69 (decimal)
2021 (rtc) → 21 (RV3028) → 0x0015 (16-bit uint) → 33 (BCD) → 21 (decimal)
Methinks rtc.set_time should actually take the full year instead of artificially constraining the input value.