According to lichess, if Black simply goes 3...Nf6 against the Two Knights Variation, then the main line is 4.e5 Nfd7 5.d4. This is the exact same position as White would have reached if they'd played 1.e4 e6 2.d4 d5 3.Nc3 Nf6 4.e5 Nfd7 5.Nf3. Why play the Two Knights at all then if Black can just transpose into territory they're more familiar with? Is it just to avoid the Winawer?
Another idea of the two knights variation is to provoke 3...d4 and get some kind of reversed Old Indian. Some players like these pawn structures, and it also may not be blacks taste to be the one with the space advantage.
[FEN ""] [Title "Analysis"] [StartPly "99"] 1.e4 e6 2.Nf3 d5 3.Nc3 d4 ( 3...Nf6 ) 4.Ne2 c5 5.c3 $1 Nf6 ( 5...d3 $6 6.Nf4 c4 $2 7.Qa4+ $18 ) 6.cxd4 cxd4 ( 6...Nxe4 $5 ) 7.Ng3 ( 7.e5 Nfd7 8.Nexd4 Nxe5 $10 ) 7...a6 $1 ( 7...Nc6 8.Bb5 $14 ) 8.d3 ( 8.Bc4 $6 b5 9.Bb3 $2 d3 $1 $17 ) 8...Nc6 9.Be2 e5 $13
Objectively black is minimal better due to his space advantage, but white operates with the vacuum which d5-d4 has created in blacks position. He will sooner or later play f2-f4 and attack the pawn chain e5/d4, for example by playing h3 and Nh2. If black takes on f4 this will isolate the d4 pawn, and white may be able to win it. Of course that will not work if black plays it sensible, for example by protecting the pawn with Qb6 and Rd8. The stronger player will win.
But as you already said, Black can play 3...Nf6 and this transposes to the main lines.
You've pretty much answered your own question. Black can go 3...Nf6 and go for the mainline, but White is managing to avoid some other lines like the Winaver.
Anyway your question could be reversed just as well: why play the main move order whne you could go for the Two Knights French all the time instead?