The Gotoh saddles are indeed a bit big and the base plate is thicker than on the typical bent metal Fender style bridge. So it can be hard to get a low string height on some basses.
I have filed the saddle slot deeper and wider for the E string to lower the string height without bottoming out the saddle on the base plate or having to shim the neck. Saddles are brass - easy to file with a chain saw sharpening file of the appropriate diameter.
Can't beat the Warmoth pricing on the Gotoh 4 string bridges.
Hipshot now makes their vintage bass bridge with an updated quick release capability that doesn't require the slotted tail. Cleaner and nicer looking to my eye. Smaller saddles and thinner base plate than the Gotoh. Nice bridge, but a bit pricy IMO. http://store.hipshotproducts.com/car...t_detail&p=210
Other sellers will have better pricing than the Hipshot online store.