I'm not an expert in this issue. But the Wikipedia article has the following statement: "There are 11 pseudouridines in the Escherichia coli rRNA, 30 in yeast

I'm not an expert in this issue. But the Wikipedia article has the following statement: "There are 11 pseudouridines in the Escherichia coli rRNA, 30 in yeast cytoplasmic rRNA and a single modification in mitochondrial 21S rRNA and about 100 pseudouridines in human rRNA indicating that the extent of pseudouridylation increases with the complexity of an organism." So at first it shows, that Pseudouridine is not something completely new in nature. It exist for a long time already. And it seems a higher amount signals to the immune system, that this RNA is more human like and not coming from a virus. Since this mechanism seems to be established in nature I think one can assume it is safe. If it wouldn't be safe, viruses would probably already exist, which would make use of this "backdoor". https://en.wikipedia.org/wiki/Pseudouridine https://en.wikipedia.org/wiki/Pseudouridine