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I'm not sure I understand your question exactly, but I'll go by what I think you're asking.

The coordinate system transformations are based on the joints only. That is to say that the link transformations have no effect on where the next joint is placed, so your stl files and where you set their origins to are irrelevant.

Therefore you must place the next joint with respect to the previous one. In the code you pasted you do not set an origin, so it will likely default to 0, 0, 0 which would put it exactly on top of the last one.