I'd choose a cabinet over a filler.

they do not need to line up with the lowers.

yes, pay attention to the backsplash, that will show any problem.

upper and lower should be flush so the backsplash tile is level.

I would leave off the window trim until you are finished and make the trim wide enough to meet the upper cabinets on either side of the window (no space) so you can tile to the trim neatly.

I'd line the cabinet you have up with the lower on the outside left edge, and end the backsplash there. Then add whatever is necessary to balance the cabinet on the right--if that's 9" plus filler, that works. But you might be able to just do an open upper cabinet there too (for cutting boards, books, etc.) and still have it look balanced while minimizing costs.

If you line up the upper cabinet with the lower cabinet, don't actually line them up. Put the left edge of the upper cabinet to the left of the lower cabinet, so that the edge of the cabinet will line up with the counter overhang. That way you won't be back here with the dilemma of where to end the backsplash. People are always asking where to end their backsplash (with the end of the cabinet, or the end of the counter) because they didn't have the foresight to plan for this.

Do you love plants or need space for display?

The second photo, but remove the upper skinny cabinet on the right, so you have equal open space on both sides of the window.

Here's a sketch to help...

Put the cabinet you have next to window with the same spacing around window. (red)

That is a good size cabinet to have near dishwasher to unload.

The remaining space to lineup with bottom end cabinet, put a cabinet there or open shelving. Use a filler if needed to get them all to end at same length.

Or flip it & put cabinet you have at end, then put 1 door opening away from sink. Ideally same size of cabinet in corner but not a deal breaker in this scenario.

Hope that helps you figure something out you will enjoy soon :)

Just a suggestion. Can both the large cabinet and the smaller one installed on the right of the window both fit to the left of the window and alight with the far left of the bottom cabinet. If they can consider open shelves in the location you currently have the smaller cabinet (right of the sink)