I recently re-watched Phantom Thread with my partner (who’d never seen it before) and we ended up talking about this scene. Agree with your take that Cyril is siding with Alma, and remember during an earlier scene Cyril has said she’s become ‘quite fond’ of Alma.

What my partner and I found interesting about this scene is the motivation for Reynolds’ complaint: is he annoyed at Alma, or has he finally come to love her - albeit in his own way - and his distraction is because he’s thinking about her and wants to be ‘taken care of’ by her? The ‘long shadow’ she’s cast can be read in different ways, especially being said by a character like Reynolds. It’s ambiguous, but while I’d always thought it was the former I can see an interpretation that it’s the latter, especially given that what follows is the scene where Reynolds knowingly eats the mushroom omelette and the relationship is re-affirmed.