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> It's because that was the Spanish flag during its age as a superpower. Spain, Austria, and Bohemia were all Burgundian realms in practice. Charles V even spent most of his time in the Netherlands, not Spain or modern Germany.
So Burgundy (!) ruled them all?
https://en.wikipedia.org/wiki/Cross_of_Burgundy
The Cross of Burgundy (Spanish: Cruz de Borgoña; Aspa de Borgoña) or the Cross of Saint Andrew