The reason you try to eliminate as much base metals as possible is because it's always easier to get a clean product from a smaller sample. It's also a way to keep the amount of waste down, making it easier to treat the waste properly.
Of course, there is a golden middle way to go, you have to know when it's time to switch method. It will differ between different persons and their situation. What works well for me is a waste of time for Jon. It's something you learn over time.
There are two main reasons the gold can come out more or less contaminated after a refining cycle, bad filtering and mechanical drag down. If you still have solid particles as silver chloride that pass through the filter it can end up in your gold. Then there is the mechanical drag down. When the gold precipitate it will lock some of the original solution between the particles and some can be stuck on the surface of the grains.
So a dirty solution with a lot of base metals will produce dirtier gold. Some of it can be mitigated by proper washing techniques but the easiest way is to have a pure and concentrated gold chloride solution before you precipitate the gold.
You also have other sources for contamination as dirty lab ware, dirty melting dish, even the torch can contaminate pure gold.
The skill of the refiner shows off in the purity of the product. I've seen Nick taking pure crap and turn it into a shining bar in one step. It was a joy to see him work.
I thought I had a handle on it, but my twice refined, first shot for a big button turned out to have palladium contamination. It took me a third refining cycle to get the purity up to where I was happy about it.
Göran