Presumably that doesn't take players and manager into account.
The -0.6% does take the players and manager into account (as it is a median figure, not average). The fact that a Premier League football club can legitimately and accurately state that their gender pay gap is negative surely means that the whole exercise is misleading.
If we didn't have a women's team, the median for women would presumably be lower and the gender pay gap figure would be in favour of men.