I like one long transom.

We did a transom on each window, s large picture window with two casements. Over three windows the individual transoms look great. Not sure why, but I think one long transom might look better across two windows. Maybe because the windows are the same size and the divider would be in the middle. Either way will look good. I love our transoms!

You don't really have room for a transom with a 48" tall window. You'll need at least 12" for a header, and even if you put the 48"H window to the counter with the counter as the sill, that only leaves 12" for a transom, which by the time it's trimmed out, is only about 7" worth of glass. Not enough to go to the extra work and expense of a transom, much less not proportionate with the window that would be underneath. Now, if you choose a shorter window, you can change the proportions and have some larger glass on top, but it also needs to work with the other windows that show on the exterior. It shouldn't be a "lonely only" in style or size.

When we had the structural engineer out to check the wall we were removing, we talked to him about installing windows too.
He said there is some kind of special wood that is used for the header that can allow it near to the ceilings. We have several windows within a few inches of the ceiling already. In our last house, we had a special kind of wood that allowed for a wider expanse then a normal header but I don't recall what that was. Before that I thought wood was wood, but apparently not.

Here are a few photos I have saved. I think they seem best when fitted directly above each window. Unless they are more decorative, like leaded or stained glass. Search transom windows on houzz for many, many ideas.

{{!gwi}}

[traditional spaces design[(https://www.houzz.com/photos/traditional-home-design-ideas-phbr1-bp~s_2107) by san francisco general contractor Dijeau Poage Construction

Going with a single transom will inevitably throw off the grilles as the middle stile between the twin casements will be thicker than the width of a grille. However, if you're doing clear glass without grilles, it shouldn't be an issue.

Sorry if it was unclear, but the width of the windows are 48 inches, not the height, so there is definitely room for transoms. I'm just not sure what look I am going for. I would describe the house as "moderately modern" and there are no grilles on any window except the front elevation. Anyone have pictures?