I am currently wrangling with exactly this and after trying both ways I would always prefer using Vue CLI completely separated. The thing is though, after going

I am currently wrangling with exactly this and after trying both ways I would always prefer using Vue CLI completely separated. The thing is though, after going through all of this I would completely skip the frontend JS mindset and just use server rendered templates. Development speed is so much faster and Turbolinks + some JS here and there is more than enough for 99% of projects.