ignition.conf and gateway.xml are always collected as part of the backup and always restored as part of the restoration.
If you don't want them overridden, you could remove them from the backup, in theory.
But it's very intentional that the simplest case of "take a gateway backup, restore it somewhere else" does its very best to recreate that exact same gateway state - ignition.conf included.
The extra files/directory workaround Phil mentioned is described in more detail by Kevin C here:
Partial gateway backup/restore (using .gwex files) is indeed part of 2027.