I did a scarf that was a similar idea. It had little motifs that were knit one at a time and attached to each other as you went. You are either knitting these from the middle to the outside or starting at the edge and knitting to the middle. I don’t think the one I did was from a chart. It had round by round directions and mine started at the outside and went in. If you think of it like making a hat in the round, it was kind of like that. There are two ways to make a hat, one can start at the top and increase and if you do the increases in the proper way it will stay flat like a beret. It may be like that. Or like a hat that is made from the bottom and when you get to the decreases may be flat at the top as you work in, it is only like the decrease part.
If your chart shows a pyramid shape I believe it will be one section of the motif, sort of like a piece of pie. So you are probably starting at the bigger part and working in. Whatever it gives you for the first row (the longest one) would be repeated all around the circle of stitches you cast on. From looking at the picture I think you are probably doing each section 6 times around the motif to make the flat hexagon shape (but I could be wrong, maybe its 12, or ?). You probably do what is shown on round 1 on your pyramid shaped chart, six times to get around the number of stitches you cast on. Then you go to the next row and do it 6 times, then the next, etc. until you work to the peak of the pyramid and the middle of the hexagon.
It may take a little blocking to make it completely flat, but it will be pretty flat if you decrease as given over each round.
Does that help?