When I change the stem direction down of the first A in the F staff; it also changes position. What is the reasoning behind this, is this the preferred way of notation? Just trying to understand the mechanics behind this. 
If you have an up-stem and a down-stem note on the same pitch, then the standard way to display them is with stems back-to-back.
With two up-stems on the same note, then it seems Dorico puts the larger note value first.
You can switch the voice order with Right-click > Voices > Swap Voice Order.
To me, the second image looks fine. (White on black notwithstanding. 
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Especially since the downstem note has a dot, this looks the best, but even without the dot, I agree that this is the typical alignment of notes in this context.
Thanks a lot @benwiggy and @Steve_Sensenig. Great advice….. Very slowly Dorico and notation is growing on me, also because of the help from this forum.
Best, robert