I've got exactly the same problem with a missing dash in the surname and I am trying to resolve it now. In fact, months ago I just ignored the missing dash in the PR document.
I was hoping the passport office will just put the dash in the British passport and take the citizenship certificate as same. If you are in hurry, I guess you can try that. I am not sure if this will cause extra money or just delay. The hassle itself might also make this not worth it. There is no requirement to get a British passport for any citizen ever, so there is no rush unless you need it. People who don't travel don't get them as they are just extra money and hassle. You must attend ceremony within 3 months of application approval, but that's separate.
Here is what I've tried so far - long. I don't have a solution or an informed opinion yet, I am afraid. However, I am not in a great hurry to get a British passport yet as an EU passport gives most rights here until at least October. You may, of course, need it sooner. If you get any insights or different experiences, it will help me in the short term and others in the long if you post here.
As mentioned instructions say to attend ceremony, then ask to change name certificate, presumably because the council already has the physical certificate. This will, of course, delay when you can apply for a passport, although you are a citizen from the date of the ceremony.
I called passport office twice. They both said both foreign passport and British passport must have exactly the same name. However, the second person started with saying that don't allow dashes in the names, but then backtracked on that. British passport policy apparently allows dash, apostrophe and space, but no other punctuation or digraphs (previous embassies have been issuing these). Google, however, finds a reference to a help page that is no longer accessible, that says that dashes are not allowed. My guess is there is some inconsistency in the passport policy and home office document issuing have picked up on that.
I also called the home office. They advised to email
citizenship.support@homeoffice.gov.uk to request a change to the invitation letter, which I did but no reply yet. They didn't mention the certificate, which I assume is already issued. I am guessing the person on the phone was not that informed on these intricacies, but I was hoping the answer to the email will be better. I don't have high hopes, though, as emails can be quite automatic answering a part of the original question (generally to anybody).
There was a post here from a couple of years for a dash between first name and surname, but this seems quite different (although the mess probably has the same cause).
Finally I looked at the barcode at the bottom of the passport. There is no dash there. The encoding is the same as a space '<' ("<<" is the delimiter between surname and other names). I am guessing a software problem connected to this is causing the issue.
British born also have dashes in the surname quite often, so I was expecting more experiences on this.
