The capacity is a compromise driven both by £ and by fitting within heritage and site constraints on elevations/roof and footprint respectively. It is not ideal but as others have noted it is still a big step forward.
I would not be that surprised if Jenrick waves this through & privately/publicly we get strong government support if we then do a Spurs like variation mid-construction to slightly enhance elevations to c 55-56k capacity. It would need revised planning sign off by LCC & another government OK but if we took this action we'd have tested that informally in advance & be confident of approval just like Spurs did.
As for leaving Goodison, game one at BMD will be the definition of mixed emotions. Excitement for a new start. Optimism for the future. A sense of loss that will be rooted in deeply personal memories, often including friends and family lost to us, for so many of us. I expect to blub like a baby despite the fact I'll be 57 if built to schedule. I won't be alone!