Some plants are too large to be grown in a single square foot of space, so the Garden Planner adds them at their normal spacings when in SFG mode.
While some larger plants, such as squash, can be trained up supports to take up less room on the ground, often they don't grow well when squeezed into a single square foot of space. This is because their roots require much more space than this below ground to access enough nutrients and moisture to thrive.
However, if you have tried this and it works for you, you can adjust the plant's spacing requirements. This does not change the size of the plant icon itself however.