The police could have had his prints from his merchandise, or an entirely separate issue, with no idea that they matched a certain until-then anonymous drug dealer known only for his posts on EncroChat.
They match those to the hand / fingers holding the cheese.
Presuming the EncroChat is anonymous, how do they then tie that to the person arrested? Where and how does that happen?
According to a link from the article, however, EncroChat was cracked last year. Stewart was presumably not one of those arrested at that time, which implies that either this crack did not yield enough information to ID him, or did not yield enough evidence to proceed against him. The former case could be solved if his prints were on file, and in the latter case, his prints might have led to additional evidence which had previously not been attributed to him.
As the article says he was identified by his prints, the former seems much more likely.