Different transform options of shape layers
Shape layers can comprise more than one shape, indeed they can contain multiple groups of shapes. So when you have multiple elements in a shape layer and want to transform one of them but not the others you use the individual transforms for that part, when you want to transform the whole layer you use the normal layer transforms.

If your shape layer only contains one element then there is really no difference, except that the layer transforms are accessible to keyboard shortcuts, e.g. P for position, S for scale etc., and work with nudging, e.g. the arrow keys or num pad + and num pad - for rotation.

Of course you can achieve the same result as having multiple parts to a shape layer by creating multiple shape layers each containing one part and grouping them by parenting, using expressions or precomping them. 

Whether you make shapes with individual parts per layer or all in one layer is a matter of taste. I tend to switch between the two, but mostly favour individual parts per layer - I like my keyboard shortcuts. 

I kinda think the AE layer shapes implementation isn't AE's strongest feature. For anything complicated I always do it in Illustrator and import.