There is a section titled "With What to Begin?" right after Introduction in Science of Logic - a.k.a Larger Logic - and there you can find Hegel's long discussion of the issue of 'starting point' in logic. I think one of the main lessons there is that 'the point of departure in reality' is for Phenomenology, and 'the logical starting point' is for Logic. (Patrick Murray (2000) understands the difference between Phenomenology and Logic in relation to the starting point in this way.)
Now turning to Marx:
As we already know so well, in Grundrisse Marx mentions two conceptual journeys, a descending one from the chaotic concrete to the abstract and a ascending one from the abstract to the concrete with many determinations; and he dubs the latter as an "obviously scientifically correct method," i.e. the abstract as an obviously scientifically correct starting point.
And as we remember, Nicolaus argues in his Preface that Marx changed his mind in Capital. InGrundrisse, the argument goes, Marx begins with an abstract category of 'production', but in Capital he abandons this method and starts with commodity. That is, for Nicolaus the category of commodity is something concrete. Of course, opposing view followed of Marquit (1977) and Carver (1980).
The controversy here is how to understand the nature of commodity as a theoretical category. On this respect, I think Chris Arthur's explanation is very interesting. He gives three criteria for the starting point: it should be i) simple, ii) historically specific, and iii) immediate. And he says that commodity satisfies the latter two but not the first; it is not simple enough since it can be further analyzed into use-value and value. What about 'value'? According to Arthur it satisfies the first two but not the third; it is not something that can be immediately grasped. Then what is the true starting point in Marx? Commodity or value?
Here we have Jairus Banaji (1979)'s wonderful solution to this puzzle: a concept of 'double starting-point' which Arthur accepts. According to Banaji, “the beginning is a movement between two points of departure.” The idea is that the commodity forms the analytic point of departure to arrive at the concept of value; and value as the ground of all further conceptual determinations (money, capital) forms the synthetic point of departure of Capital. I think this solution is also in line with Hegel's method having two distinctive starting-points.
Understood in this way, I think both of the two conceptual journeys described in Grundrisseconstitute Marx's method.
Finally, returning to our initial concern with the above discussions in mind, I think Marx's distinction between 'method of inquiry' and 'method of presentation' can be mapped into as follows:
*method of inquiry (Marx of Capital) = descending journey from the concrete to the abstract (Marx of Grundrisse) = analytical method (Hegel) = analytical shift from commodity to value (Banaji & Arthur)
-> commodity as a starting point
*method of presentation (Marx of Capital) = ascending journey from the abstract to the concrete (Marx of Grundrisse) = synthetic method (Hegel) = synthetic shift from value to commodity, money, and capital (Banaji & Arthur)
-> value as a starting point