Can I add my own trays and pots, and hide the ones I never use?

Yes: add the containers you really use, hide the rest, and your plantings only offer the formats on your shelves.

Open Farm data, then Nursery containers, and click Add container. Give it its Number of cells, Container width and Container length, such as a 200-cell tray or a paper pot chain. It then shows in your plantings’ container list. Without width and length, its trays take no room in the Nursery graph.

To hide a format you never use, turn off Visible: it leaves your lists without being deleted, and you can turn it back on any time. The containers Heirloom provides open read-only, their cells and size already set.

The steps are in Set your nursery space and containers.