Good question. I don't know. I would be speculating.
But I'm happy to speculate.
My feeling is that if the axle is flush at the end then the forks are exactly the correct distance apart. That is where it should be.
Also, if it isn't in that position, the .7mm gap between brake disc rotor and the slot in the caliper bracket will not be there. So if that is the case, after bouncing the forks, I move it. I think that brake disc clearance trumps having to adjust the fork leg position.
The left fork in my first 1300 needed to be moved a fraction after bouncing - in the early days, but not later on. My current 1300 has never needed to be moved.
But if everything else is installed correctly and the forks aren't bent, then the forks are the correct distance apart if the axle end is flush.
If they don't bounce into the correct position then something else must be preventing it from moving of its own accord.
So it might be an indication that something isn't quite right.
@Igofar had a nice post somewhere about checking how easy it is to push the axle through with one finger, and what to do if it needs that extra oomph to slide through the wheel.
One issue might be related to bearing installation. It matters which order you fit the bearings, and that order is different for the front and rear wheel.
***
If you get it the wrong way round, the wheel is too far over one way and your caliper clearance disappears.
Also it is possible to have one bearing slightly cocked.
Other issues could be the alignment of the top of the tubes and / or the relative position of the bottom of the fork legs.
There may be an issue with the mudguard fittings or the brake line fittings linking the two forks. eg if they have been tightened when the forks were not quite aligned, then it might be holding them in the wrong position.
edit - I'm not talking here about the actual metal tubes - I mean the securing of the junction blocks and/or the delay valve on the fork legs. If they were tightened before the wheel was installed ........
And then of course there is the strain put on when a previous owner has put those collars in the wrong way round.
edit - Another thought just jumped into my head. I do some things automatically these days - its just the way that I work. Most people will probably do the same, but there was a time that I didn't so - I never, ever assemble things by tightening each bolt in turn. Eg reinstalling the front mudguard. The 6 bolts are located and inserted into the relevant holes and turned just enough to hold the bolts in position. Then they all get screwed in most of the way, so that everything is positioned correctly, then at some stage they get tightened. I never leave a bolt looking as though it is tight. Its the sort of thing you do when putting wheel nuts on a car, or when tightening cyclinder head bolts. Otherwise tightening one bolt affects how the rest of them seat. As I say, I suspect most of us do something like this anyway.
I'm not an expert on this, so I am speculating. I'm wondering now whether the issue on my first 1300 disappeared when I first looked up about changing bearings and started doing them for myself. Its possible - because they last much longer these days.
*** The front wheel - install the right hand bearing first (brake lever, ABS pulsar ring side). Rear wheel install the left hand bearing first (single race bearing, brake disc/rotor side)