Yes, Sony used to report "production shipments". Those counted even consoles waiting in one of their warehouses to eventually be ordered by retail, but as you've said, they made a switch to reporting sold-to-retail numbers now. These are fully comparable to the numbers Microsoft reports.I'm also ever so slightly beginning to question Sony's ship numbers TBH. If the end user sales trackers aren't reflecting them, there's a problem. I read some posts on Vgchartz in essence that Sony counts shipped as ordered by retail, a different definition than Ms (presumably shipped to retail?). I have no idea how to verify such minutia. But the very possibility of different definitions could throw comparisons into question. Although as long as both definitions only count every console once, it should come out in the wash in the long term.
I know in PS2 era, Sony supposedly counted everything off the assembly line as "shipped". This led to inflated numbers, as apparently there could be double counting, a PS2 might be counted shipped when it came off the line in one quarter, then again when actually shipped in another. Of course again supposedly, Sony switched to the stricter "sold to retail" shipped definition this gen. They even back corrected their past PS2 shipments records to the new practice, again basically all as far as I know from reading forum posts at various times.
In any case, each console is counted once and only once. This was always the case, even in the days of reporting production shipments.
Overshipping/channel stuffing is not a big concern in the long run. The channel can only absorb a couple million units at best, and whatever excess you push on retailers will only take away from your shipment potential in the coming quarter(s). It all evens out in the end.
The same logic applies to your distinction between "shipped to retailers" and "ordered by retailers", even though I don't think there is such a distinction to be drawn in any of the figures we see here. Again, if there were, it would be momentary blips in one quarter that would be evened out soon after.