Well, that's example is also introducing dependence, which is a tricky thing of course whenever we talk about chance and stats.
But there's also another issue - a statement like "5% of positive published results are by chance since we have a p<=0.05 standard" treats every set of results as if p=0.05, whereas some of them are considerably lower anyway. Though the point of bad actors cherry-picking to screw up the data also comes into play here.
(And of course, fully independent things in life are much harder to find than one might think at first.)