What do you mean by "Unfortunately"? This appears to be the only correct conclusion from the algorithm you selected, you can't eat the cake and have it too.
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.)
Paragraph 1: I speak of a sorting method which splits the filename at the boundaries between numbers and non-numbers, and sorts by the parts of the resulting tuple, the numbers naturally (10 comes after 2) and the rest by numerical char code.
Paragraph 2: I am not sure what you mean here with writing a script. The graphical file manager shall sort its file list using the sorting function I hand over to it.
"That's not really what a graphical file manager is for". Says who? Every software which has a plugin system does that, why should a file manager not?
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.)