As long as the completions have the same annotation (the text in green) and same kind (the icon on the left), they are deduplicated.
Looks like perhaps lsp-mode generates annotations that are more useful for your scenario than the ones that eglot does. If that is the case (and not, maybe, that you have configured lsp-mode/eglot to use different language servers), I suggest filing an issue. This shouldn’t take too much time to change.
Actually, I forgot how this works in most cases X-D.
And it happens through text properties, which backends add to their completion strings. Then the
annotation
andkind
operations look them up.