Short answer: "Yes".
Longer answer... For two surfaces to closely mate, a prerequisite is that they be of the same shape. There are two potential ways to achieve their being the same shape. The first is to cut, sand, file, mold or otherwise work the shapes to be the same. The second is to apply force to deform one or both surfaces so that they conform to a common shape. Depending upon the maker and type of instrument, both methods have been employed in instrument making. Note that some materials and some differences in shapes don't lend themselves to being deformed by force.
You've created a side assembly where the gluing surface for the top is shaped into a portion of a sphere. You've created a top that is spherical in its lower bout and flat in its upper bout. The lower bout, being shaped/braced to the same size and shape as the side assembly should closely mate with little or no force/deformation. The upper bout of the top is flat while the upper bout of the side assembly is spherical. You have the usual two choices: either make the upper bout the same shape on both top and side assembly or use force to deform one, or both, to conform to the same shape. Give the stiffness of the side assembly, that isn't going to deform, to bend on edge. Given the stiffness of the flat transverse brace, that isn't going to "nicely" deform either to create closely mating gluing surfaces.
Thus, the only effective option you have - given that you want the upper bout of the top flat - is to change the shape of the upper bout of the side assembly. It should be flat to conform to the flat shape of the upper bout of the top. No amount of sanding on a spherical dish is going to achieve that geometry - spherical lower bout and flat upper bout. Achieving it isn't particularly difficult and was reasonably commonplace prior to the advent of radius dishes and building spherically domed tops. One approach is to use a flat surface, such as a piece of plywood, to which to attach sandpaper. This gives you a flat, rather than spherical, sanding board. You can then run your upper bout - only - over the flat board. You'll have a fair amount to remove from the current spherical upper bout. Marking what's being sanded and using a hand plane will speed the process considerably, rather than sanding alone.
Note that a different - not necessarily better or easier - approach is to make the top with some curvature in the upper bout that matches the side assembly and then flatten the outer surface of the top after the top has been assembled to the sides. That is, sand the necessary flat area into the outside surface of the top, thinning the top somewhat in that area to achieve the flatness you want.
Regardless, it makes success much easier if one fully understand the geometries one is creating and how they will work/fit together. This is particularly true of the neck/body juncture since getting that right by any chosen means is important to the success of the instrument.
Charles