Question:

Is the target Vault Field Layout shown in the same order as the source Vault after a Configuration Migration deployment adds new fields to the field layout in the target Vault?

Answer:

No. When new fields are added to the Field Layout as part of a Configuration Migration job, they are displayed at the bottom of the Field Layout list.

The user needs to manually reorder the list of fields so that they are displayed in the same way that they are displayed in the source Vault. 

Related Documentation:

Vault Field Layout Documentation: How to Reorder Fields in Sections