If the seam is really noticable what about epoxy putty to fill it in, something like Magic Sculpt or Aves.

Than a really thin coat of glazing putty.

Eric... 

I used Squadron green putty- lots of sanding, looked good, then primer, which showed areas needing more putty, then more wet sanding with 320 grit, looked good again, sprayed metallic aluminum finish coat and it looked awful.  More sanding thru the aluminum down to primer, used some Gunze water soluable putty for fine touch up.  Then I spent a lot of time with first dry, then wet, sanding.  Looks good now, ready to apply more finish coats- we shall see!  I think Milliput would also be a good choice, as you can smooth it in with a wet finger.

Construction tip:  Avoid having to deal with more than one seam at a time when glueing the saucer sections.  Glue two sections together, set them aside.  Then glue two more, set those aside, and then glue the final two together.  Let them set to cure for a couple of days.  You will now have three wedges consisting of two parts each.  Glue two of those together.  Then after that dries, you can add the third section, glueing only one seam at a time.  Keep them on a flat table with weights holding them down all during this process.  I used Tamiya super thin plastic cement, the solvent type, generously applied, and used many clamps to hold the seams together on the ridges on the inner surfaces of the saucer.  After all is done, I used some super glue along all the seams on the inside, just to strengthen the bond, but this may not have been necessary.

Where can you buy those putties you mentioned?  I think there must be many that are better than Squadron.  But I had a bunch on hand, and have lots of experience with it, so I knew what to expect.  Yes, it does shrink a lot as it cures.

The only problem I have with Milliput is that it is much harder than styrene, so it's difficult to sand it to a flush finish with the plastic.

At first, I was planning to leave the dome clear, but have reconsidered.  My dome is kind of foggy, not sparkling clear like the lower dome, and as the model is taking shape, I can see how it would look and have decided to paint it.  I did make the lower dome transparent blue, by airbrushing the inside with Tamiya transparent acrylic.  It really looks nice, but lately I learned that the bottom dome glows red with rotating segments when flying through space.  Darn, I could have done it that way, but it's too late now!

Also note, the ship only has three legs/ramps.  The other three are meant to be assembled closed and you should make the seams disappear.  The kit was only built this way for cost reduction purposes, as putting in six ramps allows all six sections of the saucer to come from the same mold, rather than having to make three parts with ramp opening and three without.

Here's a photo of the bottom section upside down on the table:

Chuck, You misunderstood me. The kit part fits just fine. The problem is, it is the wrong shape and size compared to the C-57D minature used in the film.  Polar Lights dome is the wrong shape and is undersized compared to the original filming minature.   If you want a model that looks like the film minature, you're gonna have to use a bigger dome that's more rounded- like a half-sphere shape rather than going up and then inward.  There are other accuracy issues with the kit as well, but the dome shape is the easiest to fix and makes a real difference in the kit's look.  If you build it as molded you get a nifty-looking saucer that looks almost, but not quite, like the film version and for lots of folks, that's ok.

 By the way, nice job on filling the seams.