X and y values in Numbers charting.

"Dependent variable" and "independent variable" are not important. You can chart X and Y points that are totally independent of each other or totally random. You can plot data where y=f(x) or where x=f(y). It really doesn't matter.

One thing to know, though is that the only true X-Y chart is the scatter chart. All the others are "category" charts, including the line chart. With category charts, the X data is text (even if it is numeric) and it is evenly distributed across the X axis in the order it is found in the table. The X axis could go 0, 1, -3, 50,20, ... or A, B, F, E, ... or 1, three, blue, 4, ... or whatever else you can imagine. Numeric X data is often evenly spaced in the table anyway so a line chart works out fine (unless you want a trend line equation).

If making any of the "category" charts, it is easiest if the x data is in the header column. The y data should not be in a header column.

If making a scatter chart, it is easiest if all data (x and y) is in regular columns, not header columns.

The same applies to charting rows of data vs columns.

"Easiest" means this is what Numbers wants and it will make the chart you want without much fuss. If you do something else, making a chart will require extra steps to reference the correct columns.