Solved. I've found how the seal effectively works and was able to completely stop leaks.
Maybe the info is useful for other folks with similar problems. Sorry for my bad english, but maybe some english/american can try it and make a tutorial
1) THE KNOWN AND EASY PART: CRACKS ON THE TOP OF THE SEAL
First thing to verify, as someone wrote in the forum, is if there is some hole/crack in the upper part of the seal. Mine has 2 cracks 5cm long in the upper part in correspondance of hooks. I inserted a 20cm piece of rubber from anothe old seal inside my seal's cracks to create a new barrier and the glued it towards the cracked part.
2) MAKING THE A-PILLAR WATERPROOF: JUNCTION BETWEEN SOFT TOP AND WINDSCREEN
I had still leaks. The same I've read in the forum, in the A pillar, in the junction between soft top and windscreen. Never read a complete resolution, so I investigated further. Adding "random" foam, searching for particular seal positions just isn't useful.
I studied my seal and mainly a BRAND NEW seal from a garage queen that never took rain or excessive sun. His seal was almost new so I could point of what was different for his water-proof car and mine.
Being sure there are no other holes in your gasket then I studied closely how the A-pillar "blocks" water to come in the juction.
The secret is not effectively the junction itself between soft top and the windscreen: this point is NOT waterproof. If you move the cover of the junction, there is a gap in it. BUT the upper part on the corners of the seal is!
I made a pic of how the water seal "work": you can see the white line I draw on it.
The white line higlights a "protuberance", a "barrier" on the seal. That major thickness ensures the soft top seal to be in close and continue contact towards the windscreen seal, creating a precise "path" for water. If this barier is in full efficieny, water can't flow in windscreen/soft top junction but is redirected to drain holes and sides of the car. So, the point I higlighted in green that is NOT waterproof itself, can't be reached by the water because is stopped before. The part I highlighted in green is not waterproof: simply it have not to be reached by the water from the upper "barrier".
So, if the upper part of the seal I draw in white works well, there is NO WAY water can flow inside the car.
If that point weakens, have cracks made removing the gasket, or the rubber becomes old.. the water is doomed to flow into your car. That explains why leaks affects who removed the seal to repair latches and maybe have cracked it disengaging from the metal angles of the cover, BUT
affects too someone who had never removed or touched it: even if that point has no cracks, the tickness of the rubber that creates that inside/outside boundary reduces due to years, temperature, sun....
So I applied a 4/5mm thick layer of neoprene to recreate that "boundary" with the shape of the white line. Water can't pass that point and reach the inside part of the A-pillar. Taht explains why in TIS there is a recommendation to verify the seal is firm in place by the plastic lugs: seal not moving ->no risk of that barrier to come looose. The cracks you can see in my seal on the lugs' compartment is not a problem (anymore), if the "barrier" towards works properly.
Washed with high-pressure water, had 4 days of VERY intense rain: no a single drop of water. Opening the top in the garage, the green point on the second pic was completely dry. No water on my foot!