A website builder will use special tools to create HTML code that makes a webpage look the way you want it, with whatever content you put in it. They generally work in isolation on a "blank slate". It may have tools that build certain functions like a "contact us" area or a slideshow.
Zen Cart uses a lot of PHP files to perform e-commerce functions, and also create the HTML page output for those functions to work within. It has many admin tools to do basic setup alterations (like turning on or off various columns and boxes), but to alter the look and feel of the site you need to edit your CSS stylesheet by hand, and sometimes edit PHP files to make more extensive changes to the layout or functions. Zen Cart does not work within a random HTML page built by something else; it does all the page building in itself.
There are many premade "templates" which you can install in Zen Cart to alter the look, feel and function in desired ways, so that you don't have to do much or any coding yourself. These templates can be further customized if you desire and are willing to learn a bit and experiment.