The knack, as I understand it, is to fit all the frame and trim to the screen. Ensure that the scuttle is secure in the correct location, and that the body is spotless and rust free/smooth. Make sure that the sealant bead is just right... Too much and the screen will stand proud, too little and it stresses the rubber trim where it clips to the frame*. Glass surface 1mm below body surface rings a bell, but I can find nothing to confirm it... Even the Thatcham Body Repair manual doesn't specify anything beyond bonding part number/equivalents.
* The main issues are either not ensuring that the bottom edge of the screen is tight against the scuttle: top corners then sit proud... Or pushing the screen assembly too deep into the body with a pattern frame: the pattern frame clip profile doesn't quite match the factory rubber# and setting the screen deep prevents the rubber from clipping fully. Fitting the rubber after mounting the screen only makes this worse... The more you press the rubber to try and seat it, the deeper the screen sits and the more the rubber won't clip in. The rubber trim coming off then becomes a self fulfilled prophecy. It is essential to have two people fitting the screen in order to correctly locate the bottom of the screen and to ensure that both top corners are simultaneously seated at the correct depth.
# another reason not to use glue or sealant on the rubber.