No, usually with something like this you would want to overwrite the files when prompted.
So then I have to delete the old ones? Considering they won't overwrite if the name is different (SAVE and saves etc)
Yet another reason why KeeperFX readme simply says 'extract to any folder' and then use the launcher to copy a few required files over from your install-directory.
But I believed the issue with the Uppercase folders had since been addressed. KeeperFX is all lowercase now right? Are you sure you're installing KeeperFX 0.4.8?
If you do for some reason want to keep the old version, or there still is some issue with different folder names, it would be probably easiest to rename the keeperfx folders to lowercase before you copy them into your GOG directory. Or just following the KeeperFX instructions of course.
devilhood, I see you're linking to the 0.4.7U version on github in the OP, instead of 0.4.8, so people might accidentally download old versions. Which could lead to the issue above.
Here's a better github link: https://github.com/dkfans/keeperfx/releases