It doesn't. J-Flash has flash loaders and sector maps for this, commander doesn't.
I'm not sure I can follow you there. As far as I recall, you can program bin files at any address, J-Link Commander will erase the sectors automatically and select the correct flash algorithm. So it has to know the flash sector map and it has to have proper flash algorithms (if that is what you mean with "loaders"). That's why you have to select the device. Actually, you can do quite a few things that J-Flash can't like setting breakpoints and the like, but I never did this.
Admittedly, the command line interface is something to get used to, but you can put all the commands in a script and execute that from a batchfile or whatever.
A 2nd problem with programming through J-Link Commander is that it only accepts binary (bin) files. However, even without a license, you can use J-Flash to create a bin from hex/mot to bin.
And of course there are lots of other tools for hex/mot/bin conversion.
Anyway, there is also a little tool called "J-FLash Lite" in the default software package that let's you reprogram through a minimalist GUI without a J-Flash license if that's what you want.
Unfortunately, whoever did this was too lazy to allow sizing of the initial device selection dialog, so you can't read the text if you're using a non-standard text size (DPI scaling > 100).
That's something you could excuse for a ten year old in his/her 1st program. Even as free tool in a commercial package, it's somewhat embarrassing. Still, it works. Any hey, you can even load mot/hex directly.
Letting aside the GUI scaling issues, the only things J-Flash Lite can't do is to dump or to unlock the device if this is needed. Then you need to go back to J-Link Commander.