Of course it is. Ligatures aren't characters, they're glyphs that represent multiple characters. Unicode does not encode glyphs, that's simply not its job. No more than encoding what font to use or when to render text in italic.
Which is the whole point of Han unification, the argument being that whether or not a particular line in U+4ECA is horizontal or diagonal is just like that. What's the difference?
To the contrary: What any line in any glyph looks like is of no concern because Unicode doesn't deal with glyphs. It deals with abstract characters that don't have appearances to begin with.
"Α" and "A" look exactly the same (at least in most fonts). But each has its own code point because the GREEK CAPITAL LETTER ALPHA simply isn't the LATIN CAPITAL LETTER A or any other Latin letter.
And it doesn't encode separate variants for unified Han characters. As in, that's not an argument, just a description of the status quo.