In metal complex electron counting, is the neutral or ionic formalism more correct?
I think, the answer to number 1 will remove the need to answer the subsequent questions:

1) Which method gives the true d-electron count?

Neither!
You cannot, and I want to stress that, derive the oxidation state of a metal in a complex solely by looking at its ligands. You can make educated guesses and in some cases only one oxidation state is plausible but there are many cases—most notably those denoted $\ce{\{FeNO\}^n}$ where such an assingment is meaningless to impossible. Without consulting spectroscopic data, it is absolutely impossible to tell whether a $\ce{\{FeNO\}^7}$ compound is $\ce{[\overset{+II}{Fe}(NO^.)]}$ or a $\ce{[\overset{+III}{Fe}(NO^-)]}$. In fact, entire papers have been published arguing one way or the other.
This essentially renders your follow-up questions entirely moot, but I do wish to take the time to point out that the metal’s oxidation state along with the corresponding oxidation state of the ligands is theoretically important information that can predict the electrochemical behaviour of a complex. The only problem is that it cannot always be neatly predicted as shown above. It is worth noting, though, that certain complexes have been assigned metal oxidation states beyond reasonable doubts (e.g. $\ce{[Cu(NH3)4(H2O)2]}$), and in such cases the predictions of reactivity are absolutely adequate.