This question ended up longer than I intended (though most of the bulk is interesting remarks by Hamilton), so I thought it might be good to include my question at the beginning before the admittedly-lengthy background:
Question: Why did Hamilton view the scalar part of a quaternion as representing time? Does the modern viewpoint of quaternions in physics admit an interpretation that involves time but does not require relativity and related thoughts as a prerequisite?
Background: It strikes me as remarkably ahead-of-his-time that Hamilton preferred to think, or perhaps insisted on thinking, of algebra as the study of a time variable. In fact, while I'm certainly no math-historian, by my reading he is actually quite uncomfortable with the relatively newfound spread of abstraction in algebra, particularly in terms of imaginary numbers. He laments on the chasm between this abstraction and the firm footing of science:
Yet a natural regret might be felt, if such were the destiny of Algebra; if a study, which is continually engaging mathematicians more and more, and has almost superseded the Study of Geometrical Science, were found at last to be not, in any strict or proper sense, the Study of a Science at all....
...and later...
The author acknowledges with pleasure that he agrees with M. Cauchy, in considering every (so-called) Imaginary Equation as a symbolic representation of two separate Real Equations: but he differs from that excellent mathematician in his method generally, and especially in not introducing the sign $\sqrt{-1}$ until he has provided for it, by his Theory of Couples, a possible and real meaning, as a symbol of the couple (0, 1).
As a solution to his quandry, Hamilton postulates that the interpretation of algebra as the study of time is the way to base algebra with imaginary numbers on a scientific footing, writing:
It is the genius of Algebra to consider what it reasons on as flowing, as it was the genius of Geometry to consider what it reasoned on as fixed.
In his treatise on the subject: "Theory of Conjugate Functions, or Algebraic Couples; with a Preliminary and Elementary Essay on Algebra as The Science of Pure Time," he develops a tremendous amount of basic algebra (from addition and ordering to indeterminate forms and exponentiation) through this lens. The sticky part is that he does not seem (to me, at least) to resolve the issue at hand; that of providing an intuitive formulation of algebra in which one can relate time and imaginary numbers, at least beyond that of Cauchy's theory of couples referenced above. And yet he himself, however, declares victory on the matter, writing that this "Theory of Couples is published to make manifest that hidden meaning." He is so taken by this point of view that he later interprets quaternions as a "scalar plus vector" as a "time plus space" element of spacetime:
Time is said to have only one dimension, and space to have three dimensions. […] The mathematical quaternion partakes of both these elements; in technical language it may be said to be "time plus space", or "space plus time": and in this sense it has, or at least involves a reference to, four dimensions.
Ever since Einstein and Minkowski (and others), it is quite commonplace to think in terms of spacetime (and indeed the concept apparently dates back to d'Alembert in 1754), but without relativity/Lorenz metrics/etc. at one's disposal, it is striking how dedicated Hamilton was to the point of view of relating time and imaginary quantities.
Question (redux): It is really Hamilton's strikingly-modern interpretation of the scalar part of a quaternion as representing time that is the basis for this question. Why did he do this? Does the modern viewpoint of quaternions in physics admit an interpretation that involves time but does not require relativity and related thoughts as a prerequisite?