Did Reynolds recognize what Alma was doing, and if so why does he go along with it?
According to the Wikipedia summary of Phantom Thread:
Alma responds by making Reynolds a poisoned omelette. As he chews his first bite, she informs him that she wants him weak and vulnerable with only her to take care of him. Reynolds swallows the omelette and tells her to kiss him before he is sick.
Reynolds knew that Alma was putting mushrooms in his food which is why she said that she wants him weak and vulnerable.
How did he find out about that and why didn't he refuse the food even though he had a chance to do so? (Could it be something like tired of trying, depression or he can get the mothering he longs for, with the fantasy that he has still come out on top?)
Could it be something like tired of trying, depression or he can get the mothering he longs for, with the fantasy that he has still come out on top?
The latter is more-or-less my take on it. I read Woodcock's fixation with his dead mother (not to mention his close relationship with his sister) as a sort of elaborate, overdetermined play on the classic overprotective mother trope.
It's here at the end that we get an additional twist on the cliche. Instead of meekly wilting as Woodcock gets bored with her and, like the muses before her, inevitably getting sent off by sister Cyril, Alma strikes back. By doing so, and assuming the role of disciplining mother-figure, she secures her role as Woodcock's life-partner in their sick (literally) sado-masochistic mother-son role-playing relationship.
Having only seen the film once, I'm not clear if Woodcock recognized the first time Alma poisoned his tea. (He's so obsessive, it's easy to imagine he did notice.) In this scene, however, it's clear that he knows what she's up to and it's part of a new role-playing game they've embraced.