Hello,
The only thing that I double check is the second chip select that is marked as NC in your LPDDR4 device. Please check that this is not an issue with your IC manufacturer.
Your RPA file is also correctly configured.
From first DDR tool log, I still thinking that the root cause is UART connection since is not able to stablish the connection.
Since it is a custom board design and manufacturing technology are different from NXP reference board, and board related parameters may differ from initial DDR script, so please try tunning:
ODTImpedance
Desired ODT impedance in Ohm. Valid values for DDR4=240,120,80,60,40. Valid values for DDR3L=high-impedance,120,60,40. Valid values for LPDDR4=240,120,80,60,40
TxImpedance
Write Driver Impedance for DQ/DQS in ohm (Valid values for all DDR type= 240, 120, 80, 60, 48, 40, 34)
ATxImpedance
Write Driver Impedance for Address/Command (AC) bus in ohm (Valid values for all DDR type = 120, 60, 40, 30, 24, 20)
Did you check signal integrity with a lower clock speed?
Best regards.