Most things should be within the same ballpark. The trouble is at the moment that CSS polyfills are an order of magnitude (or two) off native performance.
Example: Current CSS layout polyfills (like grid, regions etc) suffer from this.
Where you will see performance improvements is when developers create more expressive layouts/paints/etc. For example you can implement a grid layout with a bunch of nested flexboxes. You could also do it with the CSS Layout API. Because by using the CSS Layout API requires fewer divs, and maybe no N^2 layout passes, chances are it'll be faster.
But this really gets at the point of Houdini is to inform browsers/specs what is important. If a grid/masonary polyfill becomes widely used, then it will help inform CSS work.