The only purpose of the rivet head on the hub side of an eyelet is holding the eyelet in place until the wheel is built. It's what makes the difference between an eyelet rim and having to add washers by hand as you build.
So, if you're OK with the imperfect cosmetics than no sweat and you can build with confidence.
BTW- the market is more finicky these days, but in the past, rims commonly had a decent number of malformed hub side rivet heads.
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