Yeah, that way of making a prototype makes way more sense to me than the version I heard of.
The version I heard of was to develop a shoddily programmed / designed prototype just to throw it away and start over. Which seems really wasteful to me.
And it doesn't even have to involve any square and triangles - there are tons of free game assets with CC0 license on this site alone. There isn't any downside to using them in my opinion - other than forgetting to switch them out later or forgetting to credit the creators, I suppose.
Fully agree to the idea of modularity by the way. In the shoot em up game I'm making right now, whenever I want to switch out the sprite of a ship, I just have to add the new .png and edit a few weapon / engine positions in an XML file. Doesn't even require me to change anything in the code.