tbh - I'd rather have pads that over hang the disc than pads that don't meet the edge of the disc, that way you do not get a rusty crusty ridge on the end of the disc.
But that said it may be that the pads are not fully located down and held down by the retaining springs in the first place.
It'll be interesting to see what you find when reassembling with new springs and pads.
The big issue with pads developing a lip is that this lip can brake off and either jam the brake or reduce brake efficiency. On a bike both are really not what you want. On a car the consequences are less, but still not good.
In my view any design of disk/pad that allows the pad to sit so it is larger than the disk isn't fit for purpose.
Is it just the stock pads? Aldermog has alternative (not EBC) pads. I must check to see if this has happened. At the very least the pads need checking every 5000 miles and any lip removed. But the real answer is to upgrade the front brakes to something that is properly designed.
I think the issue with pads overlapping the disc is that as the pads wear more and more there is a risk that the unworn edges will meet and prevent the pads hitting the discs properly.
But as you say, it may be a location issue caused by the retaining clips and/or the pads. IME disc pads are not made to particularly exacting dimensional tolerances,
