As a non-mathematician, I'm not qualified to argue one side or the other nor to assess the 80 pages you ask me to consult without any explanation of where any relevant point might be found therein, nor what such a point might be.
You cited the Heaviside-Tait debates, claiming both sides were aware of risks inherent in the use of vector math, but you failed to name any such risk. Your belief that those debates documented an actual risk is incorrect. The 80-page paper I cited summarizes those debates. It also describes the history of an actual error that was made long after those debates had ended and had some influence on the crackpot interpretation of those debates. If you are unable to tell whether that error has anything to do with your argument, and are unable to explain what the Heaviside-Tait debates have to do with your argument, then I suggest you cease to cite risks that exist only within your imagination.
I asked you to give us a plain statement of the aspect of vector math you're talking about and the risk you perceive. I assume this is the best you could do:
As an information systems project expert however, I am qualified to assess experts who claim
such advantages exist, even when in the relatively small-but-famous application area of rotations, which illustrates the larger potential problem with commutativity itself.
Quaternion multiplication is non-commutative. Matrix multiplication is non-commutative. If there were a "larger potential problem with commutativity itself", quaternion representations would be just as problematic as matrix representations.
All four advantages of quaternions listed in the Wikipedia section you cited are matters of computational convenience, numerical stability, and efficiency. None of those pragmatic issues are relevant to a theoretical development of Maxwell's equations or any other laws of physics.
Even with respect to the pragmatic issues cited in that Wikipedia section, the sections that follow describe transformations between quaternion and matrix representations, warn against the potential problems, and describe practical solutions to those potential problems. Programmers may be out of their depth here, but that's why programmers of numerical computations should consult numerical analysts, who deal with such things all the time.
In our observed physical world, order matters a great deal. In the overwhelming majority of algebras in use for representation however, commutativity appears to be assumed valid and perfectly without risk for things like addition & multiplication, including when the operands are tensors.
You're quite wrong about that. Addition is normally commutative because mathematicians prefer not to use the word "addition" for operations that aren't commutative, and multiplication is commutative for fields, commutative rings, and abelian groups, but multiplication is not assumed to be commutative for rings or groups in general.
In particular, the exterior (aka wedge) product on tensors is anti-commutative, not commutative.
Fine. Now please answer: On what evidence can we reasonably conclude that in looking for sources of risk in physics research, the mathematics we use is the least of our worries?
Perpetual Student and
Vorpal have already answered that question. I will quote them and add a few comments of my own.
All of our knowledge of existence outside of ourselves and including ourselves is filtered through our use of logic. All of these considerations and discussions assume logic. What do you think mathematics is? It is extended and elaborated LOGIC. If the math were wrong contradictions would become evident. Thousands of mathematicians and thousands of physicists working throughout the world finding no contradictions in the mathematics underlying physics make it as risk free as any human endeavor. You are really out of your element here!
To expand on that: If the math used to state Maxwell's equations (or any other physical laws) were wrong, then at least some of the mathematical consequences of those equations would be wrong as well. Those mathematical consequences have been tested by countless experiments, and are the basis for routine engineering design and manufacturing of transistors, computers, cell phones, and thousands of other artifacts we take for granted. If the mathematics were wrong, those artifacts wouldn't work. Someone would have noticed.
Slightly more physically, noncommutativity of the algebra of observables can be thought of as the essential mathematical property of quantum physics. An very wide class of those algrebras, whether commutative or not, is representable as linear operators on some Hilbert space (which is of course a vector space), as per the Gel'fand-Naǐmark theorem. It's been about nine decades since it's been known that noncommutativity and quantum mechanics are essentially linked. So please understand my utter confusion about your claims about how scientists are unjustifiably assuming commutativity because there's plenty of noncommutativity in linear algebras used in physics.
BurntSynapse: I asked you to explain why you regard use of vector math (or mathematics in general) as a risk. You answered by describing your own misunderstandings of quaternions, vectors, algebra, and commutativity. Your personal failure to understand the relevant math is not shared by physicists, so your own personal mistakes do not create any risk for physics as a discipline. When physicists use quaternions or vectors properly, that mathematics is the least of your worries.