Rasterize smart object without flattening it

Sorry, i thought I was clear but I clarify what I want. It may not even have to do with smart objects, but it kind of does.

So, I use Photoshop to paint sometimes, and I'm relatively new to the program. Let's say I have my lineart (inks) and the paint/colors itself in separate layers. When I'm painting characters, I sometimes need to use liquify to fix some of their features, like a slightly tilted or elongated muzzle, etc. The problem is that if I select multiple layers, and try to use liquify, it simply gets grayed out.

Using liquify in one layer at a time is not an option because it would never yield the same results in both layers and it would get pretty inconvenient really quickly. Like i can't believe liquifying multiple layers at once is not possible, how hard can it be to implement? Other apps already do this.

Also, using smart objects feels really overkill for just doing some painting. And it doesn't let me preserve the layers if I want to rasterize it again to keep painting on separate layers. I do not want my lineart to be merged with the paint. And I'm surely not going to a separate file to edit the contents, save it, and then come back to my main file. Not only is it inconvenient but it also disrupts my workflow. 

Thank you.🙌 In the recent versions you talk about, using that option preserves any filters and transformations applied to the smart object?