I ran into this issue and took some time to explore what the underlying layout rules were that were causing it.

It turns out that CSS is very quirky in the way that it calculates scroll container sizing.

Adding an empty wrapping container is enough to make the padding be ignored.

In the end I made the parent container display flex and it respected the padding.

Here's a playground describing the issue that I built with claude: https://play.tailwindcss.com/mMfH4nM2xo