Have you toured a PCB manufacturing plant and spoken to the production engineers about what makes their job most difficult ?
Usually daft designs, but they struggle on and make them anyway.
I have, many times, but mostly working on very exotic boards with upwards of 16 layers, blind and buried vias, polyimide dielectrics, Invar constraining layers, Z-axis expansion requiring innovative through-hole plating techniques (actually no through-holes), etc. Designed to last indefinitely, exoatmospheric. So I am a bit fussy.
Here are a couple of vids. showing how a basic 4 layer board is constructed:
Take a look at the German way: https://www.youtube.com/watch?v=T7S40GYESbY
Then contrast with the Chinese way, quite possibly where your PCBs come from (they make multi-project panels).: https://www.youtube.com/watch?v=ljOoGyCso8s
Cringe worthy Mansplaining on this one.
But in both cases, note that the drilling operation is the key mechanical process, each hole drilled individually, with a physical drill. Everything else is just lamination, photo plot exposure, developing, etching, plating, QC etc. which costs the same for any design. It is drilling the holes that costs money (drill wear and machine time, let them get blunt and no amount of plasma de-smear will fix it before applying black-hole/shadow process to get the electroplating started.)
On the Chinese video, drilling is at 13”22’
On the German one, 3”30’
In both cases, rather glossed over. Because it is a key technology for commercial competitiveness, if you can work out how to do it better/faster/cheaper that gives you an edge.
If you get into commercial production quantities, you will learn this.
Just imagine the capital equipment costs of setting up a modern PCB Fab, the staffing and training costs (they have to be really good, not easy to find, most youngsters don’t have the discipline), then there are the environmental controls, all those chemicals, heavy metals, etc.
You can’t just pour e.g. copper sulphate down the drain anymore. it would also be a waste, if you might need it to plate-up things then you can, but you will need a chem-lab to control the process (you need one anyway, one skilled educated person can do that, but OMG it would be a boring job.)
Bye the way, these rapid prototyping services are stupidly cheap. They are giving away the boards for barely the price of postage and packaging, it’s really altruism, hoping to encourage young engineers, and/or get the production contract. If they had been available when I was learning I might have taken a different direction.
If you will PM me an e-mail address, I’ll send you some jpegs showing my observations. It may just be that your software has rendered the design files incorrectly, happens all the time in PCB layout.