The HC4050 has inputs that can be 5V while VCC is at 3.3V. It can not change a 3.3V signal into a 5V signal. That is why the MISO signal (data signal from SD or Flash to the ATmega) is connected directly to the ATmega and hopefully the 3.3V signal is enough.
A 100kHz I2C bus is also a 100kHz I2C bus with a 8MHz ATmega 