The Guren Mk.II did exist... Somewhat...
Oh, a few more Monoeye machines or a few more multi-eyed machines (besides 2-eyed) wouldn't hurt.
And I'm probably more for more mech-related homages, from missions to machines.
In fact, the transforming Starship idea can be considered a homage to Macross/Robotech and their massive Macross battlecarriers which are capable of transforming into a humanoid mode. However, I'm awaiting the moment when the main character can transform their starship and team up with Artix for a Macross/Daedalus Attack against one of the larger ShS warships in an impressive cutscene. Just for those that don't know, the Macross/Daedalus Attack is basically the transformed Macross punching another ship in the bridge (among other areas).
As for an Evangelion homage; the closest would probably be the ShS; being large and somewhat organic, similar to the Angels. However, that's about as far as I'd make a connection, just like Kaiju Scythe being a Godzilla homage/parody.