...this is how Blender works unfortunately, which is understandable: Once you take any of those actions, Blender won't be able to keep track of changes. The same behaviour can be seen when adding other primitives.
Although there are a lot of parameters, I decided to keep the mesh as parameterised as possible to give the most flexibility...please see the video to see some of the main parameters I use the most as well as referring to the documentation.
You can contact me through this website, visit www.markkingsnorth.com, or contact me through twitter @markkingsnorth.
The shape of the engine holes are relative to the width and height of the mid section or the sides depending on how many engines are selected. Sometimes, this can cause the engines to look thin. You can resolve this by increasing the width and height of the engines, the sides, or the mid-section.
You can hover the mouse over the parameter box and press the delete key to return the the default value, which is a useful feature throughout Blender.