Martin,
The rootstock DOES affect the scion that is grafted onto it. That is generally how dwarf fruit trees are made - by using a rootstock that "controls" what is grafted to it, essentially restricting growth. In Mangoes, if you have a rootstock that was from a "super seed", the entire plant will have much more vigor throughout its lifetime.
So, a vigorous rootstock might help overcome the issues with Black Ischia by imparting more vigor.
tmc2009
Rootstocks, in general (think citrus, stone fruits, nut trees, etc) are chosen for a variety of reasons - often for the soil conditions into which they will be planted. Sandy soils, heavy clay soils, etc, need different rootstocks.
When looking for a rootstock for figs, soils would be a factor, vigor would be an issue, RKN and other disease resistance would be a factor, etc.