Maxwell is being misunderstood. First, Maxwell makes very clear that length, time and mass are the fundamental types of units. Then he discusses a totally different convention that isn't used today, saying "in the astronomical system, the unit of mass is defined with respect to its attractive power". In other words, Maxwell is talking about a concept of mass where G is incorporated into the definition of mass.
Only in this context does Maxwell go on to state:
"For acceleration due to the attraction of a mass m at a distance r is by Newton's Law $\frac{m}{r^2}$". Then Maxwell takes $s=\frac{1}{2}at^2$ and substitutes $\frac{m}{r^2}$ for a.
So to anwser the questions:
1.Is this just per-relativity nonsense?
No, it has nothing to do with relativity. The treatise was written well before Einstein's theories of relativity.
2.Does mass being "length cubed over time squared" have any meaning?
Yes, in the context of Maxwell's discussion of a different definition of mass, which incorporates G into the definition, it is the correct unit of mass.