There's no way to stop unread messages being announced as such and added to the unread counter. Also, there's no way to get rid of the start post and the thread.

There's only thing you can possibly to do reduce the chance of this happening in the future.

Let's suppose you have contacts on Mastodon who really behave like Mastodon users. They boost everything they like. They clutter your stream with tons of uninteresting boost spam. One of the reasons why your unread counter goes to "99+" in no time.

If you want to get rid of that boost spam from certain contacts, do as follows:

• Go to Connections.
• Click on the cogwheel on the navbar, a bit to the right of your channel menu.
• Activate the per-connection filters. They're the only option available.
• Go back to Connections.
• Find the contacts that spam you with boosts.
• Edit each one of them, one by one.
  You'll now find two filter lists, an allowlist and a blocklist, just like for your channel, only that these only affect the content coming in from/through this particular contact.
• Add the following line to the blocklist:
  ?verb == Announce
  This will filter out all boosts/renotes/reposts/repeats from that contact.