It’s not that width/height are deprecated universally, but you’re correct that they’re not a valid piece of elements. We coopted them here because the tag subsequently gets transformed into a block element to which the attribute is applied.
I’ll see about adding a data- prefixed version of the attributes for validation sticklers. In the meantime, you can also pass attributes into widgets with URL parameters, so if you change the link in the embed code to, say, https://twitter.com/benward?width=450&height=600 then that should validate.
Ben