I do understand this sequence of thought! And it is intuitive (And what I'd like to think is the intent, though intent does not matter when discussing about RAW). That there is the first step (1.) that you choose between remaining stationary and retreating. After you've chosen your "step", you go accordingly to your thought process. The problem is, that by the RAW this isn't the only interpretation on the order.
You make the run roll when you pick a unit to make a normal move. BUT when "starting a normal move within 3" of an enemy" you can either remain stationary (stationary is not a normal move) or retreat (this is a normal move).
So this interpretation is also correct (by raw)
1. You pick a unit in close combat to make a normal move and declare it will run (Running rules)
2. You are now starting a normal move within 3" of an enemy. You can either remain stationary or retreat (Enemy units and retreats rules)
3. You decide to remain stationary (remaining stationary is not normal movement) OR you retreat (retreat is a normal move) (Enemy units and retreats rules)
(4. You decide to move your models 0", this counts as a normal move - Illegal when in close combat, as you have to be more than 3" from enemies after a normal move, retreat, in close combat)
What underlines this problem more, is this
As if the unit counts as moved, when remaining stationary, it would conflict with the rules of retreat (If a unit retreats, it must end the move more than 3" from all enemy units). Thus, I'd argue, it is possible to roll for the run roll, and decide to remain stationary.
I think though, both interpretations are "correct" in their own way. Which is stupid/confusing/conflicting, and should not be like that. There is nothing in RAW that completely shuts out the possibility of making the run roll and deciding to remain stationary. It comes down to semantics and interpretation on the sequence or combining the interpretation of rules regarding this exact situation (rolling for run and remaining stationary) to other rules that are not really discussing this situation (random movement, move phase generally), which is not water proof way of discussing RAW as it relies on interpretation of intent and not on exact wording of the rules.