Hi Tomo. It was this way because of one or two related factors. Firstly it was agreed that Invincible would be in mainly in charge of air defence and Hermes would be in charge of attack ops, but these definitions were not mutually exclusive and each group was supposed to cooperate with the other, so, although Hermes would get its cap instructions from Invincible, it would use its own aircraft (and vice versa of course).
In addition to this 801Sqn on Hermes had only just become operational while 800Sqn on Invincible had been using the Sea Harrier operationally for over a year, therefore while 800 knew its aircraft and its capabilities, 801 had not yet fully come to grips with it, and even regarded te Sea Harrier as impractical and its radar unreliable as they had not yet learned to use it properly. According to Sharkey Ward (hopefully in jest) the Argentines knew more about the Sea Harriers abilities than 801Sqn did
Because of this 801 decided to disregard Invincibles orders to conduct low level caps as they thought it was unworkable, so they patrolled at 20k instead, this meant that even when the incoming threat was detected the enemy had conducted his attack before he could be engaged. An example of 801's lack of faith in the radar was when, on 4th May, a Sea Harrier on CAP was despatched for a visual check on a non existant 'target', despite the aircrafts own radar correctly showing there was nothing there, while it was gone the Etendard that sank HMS Sheffield passed through the gap it had left.
The Argentine order was to ditch bombs and run whenever a SHar was encountered at low level, hence the success of Invincible in protecting its own ships compared to the horrendous losses of Sheffield, Coventry, Ardent et al from Hermes group. 801 was also providing the CAP at Bluff Cove and we all know what happened there.
801's aircraft were also under instruction to return to the ship with no less than 2000lbs fuel remaining, the figure for Invincible's 800 Sqn was 'no more than 800lbs', thisd meant her aircraft were on station 'up threat' for 20 mins longer per sortie.
The shocking thing for me is that, although Invincibles instructions were plain enough, and worked for them, nobody has had any blame attached to them for Hermes wilfully leaving the gaps in the CAP screen through which every single successful Argentine raid passed.