Flat Rate is for an Order that gets a "Flat Rate" regardless of how many Products are in the cart ...

So Flat Rate flat if set to 4.95, the shipping charge for 1 or 10 Products is $4.95 ...

Item Rate item if set t0 4.95 would charge $4.95 per item quantity per product ...

Per Unit perweightunit is designed to take the Product Weight and multiply that by the Unit Rate set on the Per Unit perweightunit shipping module, so if the weight is 4.00 on 1 Product and 2.00 on another Product, together, this would be 6.00 x the Unit Rate, usually set to 1.00 ... to make the shipping $6.00 ...

What is nice about the Per Unit perweightunit is that you can set the weight on either the Product or the Attributes to achieve a charge at a Per Product Per Attribute level ...

So, when you say "Flat Rate" ... do you mean per order? Or do you mean per Product or per Attribute or a combination of both?