In Total Commander, there is a function in the options to sort strict by numerical char code. It will sort those files correctly. Unfortunately, it will also sort "10.txt" before "2.txt". --- In all file managers, I miss an API point where one can give a userdefined sorting function for the file and folder list.
Regarding your second point, that's not really what a graphical file manager is for, I think. At this point (likely even earlier) you would be better off just writing a simple script in the scripting language of your choice. (If going for something fancy, you could also implement a FUSE based on symlinks for the original files, where the filename is prepended by a sort key. This would work for every major file manager and you could manipulate the files in mostly the same way as before.)