Fitting the scuttle to screen rubber properly is a screen out job. You can bodge it, but as you have discovered it is almost impossible to fit the twist clips with the rubber in situ, so people don't bother and then the scuttle doesn't sit right. Sealant is not a solution.
Of course you can fit the scuttle clips with the lower screen rubber in situ!
As long as the rubber is in good condition, with no cracks along the lower edge due to perishing which will cause it to split, get a trim clip removal tool that is curved, slide it under the lower edge of the rubber, and with the aid of the tool and your thumb, lift the edge of the rubber, and using a pair of curved long nosed pliers place the clip in each hole in turn whilst moving along the rubber lifting it above each hole. Before you remove your thumb from above each hole, once the clip is in place, use a large flat screwdriver to press down on each clip and turn it through 90 degrees to secure.
Alternatively remove the lower trim (carefully - don't just pull it upwards or it will tear). I lift it from one end sliding a very thin screwdriver or hooked tool under the lip that sits in the retainer, and once started, slide a lubricated piece of insulated wire along its length which lifts the rubber completely from the retainer. To refit, make sure the groove in the retainer is clear of silt, clean the lower rubber trim, and lubricate it with silicone spray or lightly with some rubber grease, and gently feed it into the retainer pushing it down as you work along its length, ensuring it is in the right position at the end you start at.
If the scuttle twist clips are very tight to turn, if is usually because corrosion on the lower windscreen panel causes the metal to expand.