These holes are actually drain holes for all the water that collects from the roof via the gutters! (it would otherwise fill the gutter between the bonnet seal and windscreen). They should not be blocked,but since this area is a major "meeting point" (body,wing,inner wing,triangle panel!!), it is number one area to develop a leak. Even worse if the R4 has been carelessly repaired there using body filler (after some time it cracks,trapping moisture...the rest is history). Roodini, I think you sealed some crack on the old sealing material "accidentally" when sealing these holes,that's why the leak stopped. But the "correct" repair can be far more troublesome as you should remove the front wings,then reseal their rear joint etc... anyway,it seems that making a R4 watertight is the hardest task...
It seems that your R4 needs its ride height reset. In my opinion its due to torsion bar sagging. It is not a good idea to use the wing as a measuring point. For years I have used the factory measuring method (chassis to ground minus wheel center to ground) and it always gives me excellent results. Renault advice the use of some special "scales" to ensure equal suspension force on each wheel,but I think it is unnecessary even when starting with all torsion bars out of the car. To overcome driver's side sagging a famous trick over here was to set both wheels of this side 10mm higher (actually permitted by the factory).