Getting in and out of the boat in 3 or 4 feet of water should not be an act requiring great skill. Many sit inside kayaks especially those w/smaller cockpits make this and act requiring skill and practice.
Since a flats fisherman may be getting in and out of the boat in waist deep water 20 or more times in a days, a low risk method of egress is extremely desireable.
The 2nd method of kayak flats fishing that I preach here at DoingStuffOutdoors, is fishing from the kayak. This method also offers many advantages. Stealth is perphaps the greatest asset of fishing from the kayak. Many times I have hooked fish virtually under the boat. A kayak casts a very low shadow and paddled at slow speed makes very little noise. A school redfish may be approached very closely and from the desired direction thus preventing long casts or cross wind casts.
The next most important adavantage of fishing from the kayak is speed. Wading is a more or less stationary method of fishing. A fast moving school of redfish will only offer a momentary target and then will quickly out of casting distance. Fishing from the kayak allows you to keep up with moving fish and make multiple casts from any desired direction.