Will Migration Assistant move all my dot files, permissions, everything?
Migration Assistant will copy everything in your home directory from your old Mac to your new one, so everything in your home directory will stay the same. 

It will also try to copy applications and other system configurations to the new system, but it will not do a complete mirror image of the previous system. 

If, for example, your old Mac is running MacOS 10.14 "Mojave" and the new one is running MacOS 10.15 "Catalina", you'll end up with Catalina on the new Mac. 

If you want on the new Mac a system as close as possible to the previous one you can restore a Time Machine backup on the new Mac. 

But I'm not sure if it's a good idea to put an older version of MacOS on a new Mac that comes with a newer version of MacOS - it may not work as expected. I'd recommend to try the Migration Assistant way instead.