While I myself would be taking the Markdown approach as well, it’s worth noting that Scrivener (or as noted, the text engine) does support cell merging. You have to use the floating palette, so right-click in a table and use the Table ▸ Table... contextual menu command.
- Horizontal merging is straight-forward: just select any amount of text from the adjacent cells you want to merge into one.
- Vertical merging is a bit more awkward because selection is more text biased than cell biased. You’ll see what I mean if you try to select a column. To do that, you need to hold down the Option key when clicking and dragging, which invokes the text engine’s “box selection” mode.
With a valid multi-cell text selection made, the “Merge Cells” button will light up in the palette.