Lizzy can't seem to account for Charlotte's evident cheerfulness except by supposing that the novelty of having her own home and henhouse hasn't worn off yet. But remember, we are seeing all this through Lizzy's viewpoint. I'm going to take an unpopular view here and suggest that maybe Charlotte, who has described herself as "not romantic" and who is married to a guy who's a bit of a pill, has been swept off her feet by Mr. Collins' attentions to her and and is just as awed as he is, though in a classier way, by the regular invitations and visits from the ladies of Rosings. I'm sure Charlotte has never had so much attention in her life and wasn't expecting so much.
Consider this: She's starting to form romantic schemes for Lizzy, and even Mr. Darcy, who certainly would have found Charlotte too plain for his taste just a few months ago, feels moved to say that the house is comfortable and that Mr. Collins is fortunate in his choice of a wife. I don't think Charlotte would be able to put up such a good front around her sister, her best friend, and relative strangers if she weren't at least content with her lot. An unhappily married woman wouldn't be wishing her best friend would find a husband.
As for the house itself, Lizzy gives Charlotte credit for encouraging Mr. Collins to garden, thus keeping him outside a lot, and for using a sitting-room that's in the back of the house while Mr. Collins' library faces the front. But remember, Mr. Collins lived there alone for a time, and he probably would have preferred the front-facing room for a number of reasons -- the light, the view, and the fact that he can see when Lady Catherine is driving by.
Charlotte says she encourages the gardening for the exercise, which could indicate an interest in Mr. Collins' health. When we first meet him, he is described as "heavy," and maybe she's trying to keep him alive so he can inherit Longbourn. It could also be that they need the vegetables he grows.
And Mr. Collins, while he is pompous and foolish, isn't a total idiot when it comes to his domestic comforts. We learned earlier that he installed some shelves in a closet, and now we learn that the garden he cultivates is well laid-out. I think that when Mr. and Mrs. Collins do come into possession of Longbourn, they will make it much more prosperous than Mr. Bennet has been able to do.