My understanding is you make fewer but more replicable mistakes. If you use a wire you have to trace it, keep the length consistent for timing reasons, use very consistent soldering technique, and ultimately you have a hard time tracing issues. With a homemade PCB you generally do get what you ask for in terms of circuitry. Traces are the right length, right thickness, right spacing, and if not then the whole board is similarly impacted, so it is obviously broken or not broken. If you mess up your design then you have a problem, but if you did the process right and you have a valid design then it works.
That all said, homemade PCB is a large time sink and modern PCB manufacture is so cheap and fast it doesn't make sense to do at home for the most part. You can literally get a complex board faster by ordering it from halfway around the world and having it posted than making it yourself. I would say it is a good learning exercise, not a good manufacturing or prototyping practice.