I’m not sure what you are asking? Is the problem the doors and thus the “trim” aren’t all the same size squares? Shaker style doors come in all sizes. The raised edge is built into the door and follows the shape of the door.

You really have to have the cupboard sizing and doors to accommodate the recessed squares. For instance in this image the top row of cupboards, each cupboard door (and the cupboard behind) is a perfect square.

It looks like the plinth at the bottom and the shadowline at the top were adjusted in height to accommodate this, rather than adjusting the "frame" on the door. God is in the details, and this means that the nice detail that you want can't be applied as an afterthought, but needs to be allowed for when the cupboards are designed.

Best of luck, Dr Retro of Dr Retro House Calls and Dr Retro Virtual Visits via Zoom

Put a bulk head above cupboards