What backup solution is thorough enough to include low level stuff like homebrew? Is Time Machine thorough enough?

I need to migrate to a newer macbook soon, because my current one is falling apart. But I have a lot of lower level stuff installed / configured. Such as homebrew formulae and casks. And also configured defaults in terminal like defaults write com.apple.finder CreateDesktop false. I’ve also deleted my normal Downloads folder and replaced it with a symlink to a Downloads folder on my iCloud drive. And I’m using mackup to replace most of my apps’ configuration files with symlinks to my iCloud drive as well.

So you know, a bunch of low level stuff and uncommon customizations. Will Apple’s default tools be thorough enough to include those as well? Like Migration Assistant or Time Machine? If not, what are they likely to miss? I don’t mind having to redo some things manually, I’m just worried that I won’t know exactly what Migration Assistant (for example) missed and that a few months later I’ll be scratching my head about why something isn’t working the way I was expecting.

If there’s another tool that you’d recommend then I’m very interested.