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Lacerte is following the instructions for F.1040 but it is a bit of a surprise because nowhere in Sec. 2204 of the CARES Act or in the JCT report does it say or imply that the $300 limit for "any individual" would have to be split in the event they are filing MFS.
I'm inclined to believe that the IRS misinterpreted this and the filing instructions are incorrect.