Change the oil/filter on the first change always, regardless of miles. Later on after 20-30k if you want to change oil without changing filter it will not hurt anything, as long as the filter change does not exceed the required / recommended interval. I recommend first change at 3 or 5k. That is just my opinion based on years of engine building and performing oil analysis. I do not have any scientific data to base that on.
Toyota does in fact run the engine and change the oil on brand new vehicles, but this is nowhere near an engine break-in. It is mostly for camshaft break-in (most critical time for camshaft is first 20 minutes).
Your engine will not be broke in for several thousand miles. Mainly for seating the piston rings to the cylinder walls, main, rod and camshaft bearing break-in.
I have changed the oil in my Z-71 many times at 1/2 interval without changing the filter due to oil color from heavy pulling (fuel contamination). There is a completely separate (and costly) test for that, so I just change it. A high quality filter will easily do its job past the change interval as long as the engine internals are in good shape. If you are clogging an oil filter after 10k you have a lot more serious problems than dirty oil.
As a certified oil analysis operator on military aircraft I will tell you that oil can be good after many miles (hours for aircraft etc.), but will never be as good as new oil. Oil degrades with heat, metallic particles and contamination. Oil analysis looks for wear metals in PPM (Parts Per Million) and cannot be seen.
I look at it like this;
Oil/filter change recommendation is 10k
Change oil and filter at 10k = minimum requirement
Change oil only at 5k, oil and filter every 10k = above minimum requirement
Change oil and filter every 5k = well above minimum requirement, does not scientifically guarantee a longer engine life, but makes some of us just feel better.
I would rather buy a used 4Runner that had the oil changed every 10k and driven responsibly than one changed every 5k and beat once in a while.