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The edge of the flat-top at the ejection port is very sharp and I think it's digging into the holster when drawn from a particular sitting position.

Hmmm... The flattened portion of the top of the slide is wider than the sight channel in the holster?
Is there leather shavings on the gun in that area when you draw?

I have a Safariland retention holster for my Sig p239 and there's a trick to drawing the gun from it. Yesterday I discovered by accident that if the holster is not on your belt and on your hip, i.e. loose on the table, and you insert the gun, there is no way on this planet that you're going to get the gun out. I was wrestling it and cursing it when I heard a noise. It was my wife standing behind me snickering.

Yikes! That could have certainly had disastrous results.

Everyday before I leave the house, I draw and press check. It's a good habit imho.