It is not a quality difference but is a size and style difference. The standard size shutters come in a couple of styles, two widths and several heights and are out of a mold so labor costs are lower which makes the price less.
The custom size shutters come in many different style configurations as well as heights in 1/4″ increments and more widths; They are component built so there is more labor involved which is why the prices are much higher. The bottom line is if you can get the size and style of shutters you want in the standard size shutters then there is little reason to get the custom size shutters. If the style/size you want is not available in standard then you don’t have a choice but would go with custom size.
NOTE REGARDING MIXING STANDARD AND CUSTOM TOGETHER:
The standard and custom are compatible however they are not the exact same since the custom size shutters are component built instead of out of molds like the standard shutters are. The custom could have different size top, middle and bottom rails along with other small details that are different. So people do use standard and custom Mid-America Shutters together since the color and general appearance is the similar however don’t expect them to be identical.