I don't really know anything about Eraserhead, but Clerks and Napolean Dynamite have very minimal locations which obviously cut down on costs significantly. Their plots were likewise very minimal and ordinary (which is why they resonated with so many people), which further kept the budgets low.
Even if you ignore that everything about Maradonia's existence is to make money and that the passion ended when Gloria's parents forced her to expand the story and include excessive Jesus shit in it, it's still a much more ambitious project. It's akin to trying to make Harry Potter or Lord of the Rings with next to no budget. And as Ralph Bakshi's Lord of the Rings (Part 1) shows, no matter how much passion you have for the project, the end product will always be shit without the budget (or time) to go with it.