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I can't see the new Apidura design online but the older one is made like I'm talking about. I guess it looks a bit neater but I found when you pack it you don't end up with a flat transition between zip and fabric. I also think you'll pull your stitches through the fabric when it's full of stuff because of the directions you are pulling in.
on a side note adding foam around the sides helps a lot to hold shape too.
A few tips from my relatively limited knowledge of making bags, get some double sided tape like this for your seams, it makes things easier to hold together so you can get straighter lines etc. https://www.profabrics.co.uk/products/double-sided-seaming-tape-6mm?variant=6056078531
And when you do the zip, I think it's easier to fold the seam over and stitch it onto the zip through the seam and through the zip (3 layers of fabric). Difficult to explain over in text but if you look at something like a revelate they have a stitch running along the zip which might make it clearer. You can also do this on the zip ends too.