does that combination seal better than the soft top door plus sliding window? I'm wondering if the issue is the 2 piece doors on the soft top and flex at the top or if it's the seal on the fiberglass top.
Door seal, no matter what you run, is a bit of voodoo. It's dependent on door alignment, tub-to-bulkhead alignment, top alignment, gutter alignment, etc. if any of these are misaligned, you may get leaks, a sticky door, a difficult-to-open door, or a door that pops open while driving.
I've never had major problems with door tops fitting badly, and the technique I've described somewhere using strips of pond liner helps tweak the fit between the top and bottom. I've heard of people having more serious problems and actually hooking their door tops to the visor to hold them in. That was described here in a super old tips post. I think that's a bit much though an snakes me think something more significant was messed up.
Do you have one-piece seals on your hard top? (There should be) if so, how is the transition between the body and the top - this needs to be as continuous as possible for the seal to bridge the gap nicely. A picture of your door jam and door seal would help a lot.
I had a 1997 with the fiberglass hard top and I was OK with the door seals. Didn't understand that complaints. I actually really liked that top.
I've got a 1995 now with only the Rover's North top and I haven't even tried driving it with the windows yet. If I get another fiberglass hard top I'd probably have to repair it and paint it body color at which point it may be justifiable to get the SW doors and get those painted as well. It's not the door seal I don't like about the sliding windows it's the sliding windows and lack of place to put my left arm.
It's mid to late September in Austin with the temps still in the mid 90s but it will eventually be roof season.