Is an alpha particle four nucleons or dodecaquark? In a $\alpha$ particle, do the 4 nucleons stay distinct in any meaningful manner, or is it more accurately considered to be a hadron composed of 12 valence quarks that are not subdivided into nucleons?
I presume the answer is similar for $^2$H $^3$H and $^3$He. For heavier nuclei, Pauli exclusion appears to force internal structure of some sort.
 A: According to this link the binding of the quarks in the protons and neutrons is much stronger than the spill over color forces, the nuclear force, combining into the alpha particle.

The structure for the alpha particles can almost be considered crystalline like in state. The sections on the "Deuteron & Alpha Steps” illustrates how the progression of stable nuclei can be visualized as deuteron or alpha building. The table of stable elements shows a construct similar to what would be created by a long chain organic polymer or the deposition pattern of a crystalline sub-straight. The pattern of stable nuclides is indicative of filling crystalline subsets as well as building a larger crystalline set. This statement will become clearer as you proceed.

So no, nuclei are held together by the residual  color forces between protons and neutrons, modeled with pion exchange.
A: Definitively 4 distinct nucleons. Combinations of more than 4 quarks have never been observed. The existence of tetraquarks is pretty much confirmed [1]: the so-called Z(4430) whose quark content is $c\bar{c}d\bar{u}$. The next-lightest candidate, the pentaquark, has been entertained but the conclusion is currently that it does not exist. So 12 quarks!
Interestingly, note that the tetraquark mentioned above is heavier than an $\alpha$ particule (4.4 vs 3.7 GeV/c$^2$). The putative pentaquark resonances have masses around 4.4 GeV/c$^2$ too. Thus even without all the evidences provided by a century of nuclear physics which point to the fact that $\alpha$ particle are made of nucleons, clearly a dodecaquark would be far too heavy…
[1] https://arxiv.org/abs/1404.1903
