'Theory' is used by both scientists and philosophers, and the nature of space and time is still very much the domain of the philosophy of science, as opposed to science proper.
According to the Online Etymology Dictionary, the vernacular 'theory' comes from Latin:
1590s, "conception, mental scheme," from Late Latin theoria (Jerome)
The language communities of science took that term, and adopted it to their own needs as often done by technical disciplines when creating their own technical language to eliminate linguistic ambiguity. Thus, closely related parallel usage remains. The nature of time is still very much a topic for discourse in the philosophy of science and as such propositions about the nature of space and time are very much alive metaphysically. Argument of what is the essence of space-time is still a question for the philosophy of space and time, and while physics deepens our conceptual understanding, it does not replace it.
Words often vary historically in meaning and multiple senses often emerge to be used in slightly different ways. The nature of time, despite its use as a fundamental unit in physics, is still highly metaphysically charged. As one of the SI base units, time is taken as a conceptual primitive. Philosophy is still a means by which primary concepts in other fields are examined, and time is no different. When one asks "what is time?", one has left physics proper and entered into the discipline of philosophy of science. Time is not only used as a primitive in physics, but in chemistry, biology, and any science derived from or related to them. Psychologists have an interest in the neurobiological origins of time because time is related to perception. One very famous philosopher who has a very specific reading of time is Daniel Dennett who in his Consciousness Explained devotes an entire explanation in Chapter 6, Time and Experience. Philosophy of mind is greatly interested in the relationship between the phenomenological and what Dennett calls heterophenomenological (read objective) aspects of time. Even if one grants that empirical studies of how the brain behaves while the mind experiences time inform, they wouldn't be able to account for the experience and conceptualization of time fully.