According to section 9.5(12)(2):
"Align the items along the main axis per justify-content."
This step precedes section 9.7, "Resolving Flexible Lengths", in the algorithm's order. This sequence implies that the effect of justify-content might be overridden during the redistribution of available space.
However, it seems more logical that justify-content should occur if there is remaining space after the flexible lengths have been resolved.
According to: 8.2. Axis Alignment: the justify-content property:
The justify-content property aligns flex items along the main axis of the current line of the flex container. This is done after any flexible lengths and any auto margins have been resolved.