Issues faced by the printer: 1. Ext 1 over extruding. Extruding twice what it is supposed to extrude.
Cause of Issue
1. Marlin 1.1.9 was uploaded for the board with Jumper config for TMC 2209 (non-UART)
2. On the board jumper setting was for UART

The jumper configuration was wrong. The correct jumper configuration for non non-UART setup is different.
“By installing the UART firmware, this issue was solved.”
3. Ext 1 was overextruding. Checked by seeing single print using black and white filament (to make sure it wasn’t filament dependent). And then seeing the length of extrusion (how much filament moves in when pressing 10mm extrusion), E1 was moving 20mm filament when 10mm was being pressed.
Resolution:
Since the UART firmware itself had bugs,
1. Code was compiled from GitHub https://github.com/FracktalWorks/Julia-Pro-Dual-Marlin-2,
2. Print was not starting initially, because the M420 S1 in the start g-code goes into an infinite loop of bed leveling mesh does not exist ( should be fixed in the future)
3. Did G29 separately, stored the mesh, and then the print started.