Software modifications are no longer needed because pins_BTT_SKR_MINI_E3_V3_0.h has been modified accordingly.
SKR Mini E3 V2/V3 have 3.3V logic but LCD screen is adapted to 5V microcontrollers so appropriate modifications are needed.
Schematic of the 2004 LCD with the modification included:
To drop down the voltage from 5V to 3.3V you can use linear voltage regulator or simply a zener diode and a resistor like in the photo below.