Exclude option?

Not automatically, but you could append a class “nolightbox” to these video links to prevent them from opening in the light box…

How would I add that class to a link?

In the current version, you’ll have to do this manually like this (assuming you are using the new block editor):
1. Open your post for editing and find and click the paragraph block where your link is
2. Then click the three-dots menu in the paragraph block tool bar and select “Edit as HTML”
3. Now find in the HTML source code of the paragraph your link and add class="nolightbox" so it looks like this:

<p> 
...
<a href="..." class="nolightbox">...</a>
...
</p>

Note: in the next plugin version, adding the class in the block Advanced > Additional CSS class(es) field will also be possible.