"... I was assuming that you take, say, 1000g of vinegar and neutralize it to make a mix of "water" and sodium acetate...."
But, with respect, that's not what PJ did -- she said she added 96 g NaOH to 100 g vinegar. She didn't first make 100 g of sodium acetate solution and then find how much NaOH she could add to that solution. Based on what she did, the total % of NaOH added to the vinegar was about 48.5% by weight of solution, but some part of that NaOH is acetate and some is not. Without doing the math (or another experiment), we don't exactly know those answers.
"...Would you not be able to make a 45% solution with that?..."
You'd have to back-calculate how much of that 96 g of NaOH she added was converted to acetate. That will tell you how much of that NaOH is still available for making soap. In other words, is the NaOH consumed by the acetate reaction 48.5% - 45% = 3.5%? If so, then yes, you can make this solution the way she did it and get an effective 45% NaOH solution for making soap.
Most people, and I imagine PJ is among those, won't want to look at the problem in two steps - (1) neutralize the vinegar with NaOH and (2) add extra NaOH for their soap making masterbatch. They will want to measure vinegar, measure NaOH, mix the two, and know the % effective NaOH available for soaping, which is something less than the % total NaOH added to the mixture. The formula can be adjusted to spit out that number.