I'm not really sure the difference between what Disk Utilily does and what the chown and chmod commands do.
Disk Utilily's "Repair permissions" looks at a database that's stored somewhere in /Library, I believe, and which lists the "correct" permissions for many files, mostly those supplied by Apple. If the actual permissions differ from these, they can be reset.
Those "correct" permissions are sometimes necessary so that the OS function operate at all (e.g, if some executable files have the wrong owner, they might not work), while other permissions are only required as a safety measures against hackers and malicious programs trying to "break in".
As for the permission of the Extension (and Extra) folders, they are mostly not important because when they get loaded as part of the early boot process, their permissions do not matter at all. Hence, while you are trying things out with different kexts, it's easier to just change all permissions and/or owners of the folders to "read+write" for "everyone" so that you do not have to authorize changes all the time.
Once you're doing testing, resetting the proper (safe) permissions would be prudent.