Totally an unfair comparison. First of all the Germans were operating from bases quite a bit further away from Dunkirk than they would have been operating against Southern England during Sealion. Not only that, but this was after a huge expenditure of effort against the French and British ground forces at an extreme tempo of operations for over 2 weeks previous, meaning that operational rates had dropped tremendously, not to mention the losses incurred in defeating the Allied air forces on the continent. Also the LW was busy at the same time operating against the French and other allied ground forces in the pocket and outside of it too. The weather was pretty bad during the evacuation, meaning the LW could only operate 2 of the days of the evacuation, both of which were not at the peak of the 'packed' ship period.
This is not comparable to the situation during Sealion, as the LW would have had time to rest, would have good weather (as they would be launching it during a period where shipping could operate), have much, much closer bases to the Channel, so would have a much higher turn around time between sortees and less fatigue traveling to the fighting area, and they would have air superiority over the Channel (as the prerequisite for Sea Lion is defeating the RAF in Southern England), which they did not have over Dunkirk, as the RAF was sending over fighters from England to cover the evacuation that was closer to Dunkirk than LW bases. Plus here the entirety of the LW would be available, rather than a fraction at Dunkirk.
The situation would be very different, meaning the Dunkirk experience is not useful for comparison at all. Even the fighting around Malta isn't instructive, as Malta was much further from Axis airbases than the English Channel was from German bases in France, Belgium, and the Netherlands. The LW is going to have much, much more in terms of aircraft to throw at the British as they advanced into the constricted area of the Channel mere tens of miles from LW bases in the Low Countries. As the Kanalkampf demonstrated the Ju87s were more than capable of shutting down British shipping during daylight hours even when covered by the RAF, which the British fleet would not be here, as again the premise is that the RAF has been defeated in Southern England as a prerequisite for the invasion to even be happening in the first place.