I read Lovecraft quite some time ago and I can’t claim to have a perfect memory of it… And then I played the Fantasy Flight boardgames, which probably took some (necessary) license with the content, so I might well be mixing things up even more…
However, I recall there were several themes in Lovecraft.
One was indeed the Ancients, as in the Mountains of Madness, that were huge. But then there were the contemporary worshippers of the Ancients that sometimes accomplished some sort of transformation to resemble them (Shadows over Innsmouth? ) and they would be more or less humanoid.
Then, IIRC, there was a story where Dagon got rammed by a ship [and no, I’m not referring to the Call of Chtulu FPS where the main character shoots him with rockets or something…]
In any case, Phoenix Point is not set in the Lovecraft universe, rather a universe where his life’s work has a terrifying explanation… Which is, by the way, genuine Lovecraft… this mixing of real and fictitious elements until the reader is not sure which ones are which.
And yes, there are problems with maintaining the Lovecraftian horror theme with the currently existing balance issues…