Hello @Gajju ,
MERGE INTO is not being deprecated, APPLY CHANGES should be seen as an enhanced merge process in Delta Live Table that handles out of sequence records automatically as shown in the example in the documentation shared.
The notion of wrong results is pertaining to handling out of sequence records which may be prone to errors due to logic implementation in MERGE INTO
MERGE wins when you you need full control of out of sequence without built-in sequencing feature use cases
Regards