Uniquifier = ROW_NUMBER() OVER (PARTITION BY NewName ORDER BY SchemaName, OldName, NewName)

Note I added OldName, in order to prevent spurious flipping back and forth.

Test parameter:

@IndexConvention = 'IX_%INDEX_TYPE%_%UNIQUE_INDEX%%FILTERED_INDEX%_%TABLE_NAME%_%INDEX_COLUMNS%'

FROM

sys.indexes i

JOIN sys.tables t ON

i.object_id = t.object_id AND

i.type_desc IN ('CLUSTERED', 'NONCLUSTERED', 'XML', 'SPATIAL')

AND t.is_ms_shipped = 0

Note I added AND t.is_ms_shipped = 0 to exclude IsMsShipped objects.