While the idea of linguistic asymmetry predated the actual coining of the terms marked and unmarked, the modern concept of markedness originated in the Prague School structuralism of Roman Jakobson and Nikolai Trubetzkoy as a means of characterising binary oppositions.
Andersen, Henning (1989). "Markedness—The First 150 Years". In Markedness in Synchrony and Diachrony. Berlin: Mouton de Gruyter.
Halliday glosses 'unmarked' as neutral, default.
Markedness is about choice in a system: neutral/default or notable, whereas congruence is about the stratal relation between meaning and wording: in a congruent realisation, the meaning and wording agree, and in an incongruent (metaphorical) realisation, the meaning and wording do not agree. Markedness is about systemic choice, congruence is about intra-content realisation. A Theme can be unmarked or marked, but not congruent or incongruent, since there is no such thing as textual metaphor.
