It sounds like the rubber bump stops are screwed in, so they are not touching the underside of the bonnet...!?
The bonnet is basically held down in the middle by the mechanism. The front outer edges of the bonnet can then move a little like a sea-saw... the rubber bump stops should lightly press against the underside of the bumper when the bonnet is closed, this is to stop movement, but also by adjusting these you can affect how the bumper settles, and therefore its alignment.
It may be that over time the bump stops have screwed downwards, or become worn allowing the bonnet to move freely...
is the offside slightly low? when you push down the nearside does the offside lift slightly?
if so screw the offside rubber bumper out so it hold the nearside lower.. this should lower the offside.
(in short, adjust the bump stops so they touch the bonnet underside and hold it level.
If its high, either it needs adjusting in the way, or the offside needs adjusting out.
Its difficult to explain but if you start moving the rubber things it'll become fairly obvious. They don't require a lot of movement for the bonnet to move a fair bit
If the bumps stops are all screwed in fully (so they are lower) then they are not supporting the bonnet. The bonnet is then held in place via the mechanism in the middle, but the other corners are free to move. There is a fair bit of movement in such a large panel and so screw out the bump stops so they are slightly compressed when the bonnet is closed, and adjust these to get the bonnet level,
if you are finding that you cant get both sides level and low enough to align correctly, then im sure you can adjust the bonnet locking/release mechanism so it sits lower.
In my experience most leon bonnets sit a tiny bit low when compared to the wing panels.