When applying constraints to the design, the commands read_xdc and source differ in behavior.
The constraints applied through the command source are
always saved inside the checkpoint after the constraints applied through the command
read_xdc. To preserve the XDC constraints inside the
checkpoint in the same order that they are applied to the design, use read_xdc -unmanaged instead of source.
For more information, see the Vivado Design Suite User Guide: Using Constraints (UG903).