I admit, I'm not much of a lady, but I'll toss my two pesos.
She's right, it is more comfortable without clothes, and in her own home, absent visitors, there is no reason she needs to be dressed. If this bothers you and your husband, avert your eyes.
Both of you are unreasonably fastidious about her being clothed. She can't even sleep in the altogether! It's no wonder that she rebels against your unreasonable insistence, and even bullying. I would, too. This is modesty driven to a mad extreme.
She needs clothes on when she is away from home. She's already developed a modicum of modesty as she wears underpants even at home, and that is sufficient.
This is a battle, a rebellion, of your own making. The small skirmish you and your husband started has become a war. It is time to negotiate a peace treaty -- consisting mostly of your allowing her freedom of choice.
For a time you will probably continue to have a battle over dressing when she leaves home, but this will pass quickly if you are more reasonable about what she wears, or doesn't wear, at home. Don't keep making it AN ISSUE.
It could not be more normal for a child to want to be unclothed, or barely clothed, and comfortable. What you should be teaching her is that, within reason, she is the master of her fate and the owner of her body. And her preference is well within reason. She's a great deal more savvy than you credit her for. She knows that everyone wears clothes in public, and that the problem with what she wears at home is of her parents' making, not her own.
It is much better to cultivate a relationship of tolerance and cooperation than of dominance and either submission or rebellion. You don't want her to define her clothing tastes in terms of what gets under the skin of Mom and Dad, or what you experience at age three will be played out much more ferociously, and scandalously, at ages 12, 14, or 17.
To what end must she be clothed at home? To be comfortable? She is comfortable nearly naked. To check the immodest thoughts of her parents? That is not her problem, it is your problem.