I know exactly what you are talking about, and coming from another person who questions things like this and needs clarity to move on I thought I would add my 2 cents.
Agree that there is no specific forumula for the stance - as long as it enables you to align correctly, you are in balance, comfortable, etc., then just personal preference. However especially when learning or using an aiming system, you stance or PSR may need to change slightly to enable the new visualization process.
The way you step into your stance can have an impact on how you perceive the relationship between the CB and OB. Even a foot or two of distance will change your eye location and the relative size of the balls slightly, and if using something like SEE it will slightly change the sizes of the shadows as well. If sighting from your set position, you can just bend down into the shot but may not have a great perception, a feeling of being too close to the shot, etc. But if you step back slightly and walk into the shot, your perception might be slightly better but you need to take more care when stepping into the shot, as stepping in offline can ruin the visual perception you built initially.
Personally I've tried both ways, for me I've found standing just slightly more than a cue's length away to be optimal, I get a good balance of visualization and closeness to the shot. Once I'm locked in, I take a slight step in with my back foot and then step forward with my front foot and bend down into the shot. I would tell you if you still are having issues just try both methods alternately and work with them, one should emerge as the one which fits your visualization and approach the best.
Scott