The similarity-checking software does check against posted preprints, which are permanently accessible with a registered DOI. When a journal is running this similarity check, they should review the match and realize that it matches to your own registered preprint, which is allowed by many journals.
For this reason, we recommend that you declare in your cover letter that you have a registered preprint online and provide the link so that the editor is aware of it before the similarity check. If a journal notifies you of the similarity to your posted preprint, it may be helpful to respond to clarify that the similar manuscript is a preprint of that paper and thus is still unpublished.