Your programs aren't installed in your home directory unless you put a self-contained package format like an AppImage in it. But settings for them usually are, if they're desktop programs anyway. Server programs are a different kind of beast. Browser bookmarks are in there, in a hidden folder.
If it's suggested to copy over your files in your home directory it's to retain those settings. That's not a bad idea if you don't have /home on a separate partition.
Anyway, to get back to your question, whether or not hidden files are copied depends on how you copy them. If you're doing it graphically, what you see is what you get copied/moved. So if you can see it and select it (kind of hard if you can't see it) then you can copy/move it. So if you need to move just certain hidden files, for example, you need to turn the 'view hidden files' option on so you can select them. But if you're copying/moving a folder, everything in that folder, including hidden files/directories will be copied/moved, too no matter whether the option is on or not. So the easy way is to to just move your entire home folder somewhere (e.g. move the folder 'bill'). Don't move the entire /home folder or you could end up with /home/home/bill which would make Jason sad.
Incidentally, if you copy files on the command-line with the wild card or even the folder, you won't like the results. The hidden files/directories don't get copied. Geeks use 'rsync' for that but that's beyond the scope of this post.
I'm not sure what's going on with your screen. Check in your settings to see if there is a brightness control under your energy settings. Sometimes you can control the brightness there. Sometimes you can't. But it may be why you can't adjust the brightness in the usual way (the notebook keys) because it took it over.
Btw,
this website claims to show you how to upgrade from MX-19 to MX-21. You have to be comfortable with the command-line to do it and I haven't tried it myself. It might be worth a shot. In any case, this would be a good time to use an image tool to get back if something goes awry. You can use include your /home directory in Timeshift but remember that if you restore it, it will clobber any existing files you already have when you do so, not just the system (i.e. Linux system and programs) folders. Don't use it like that way normally for that reason.