First of all, thank you very much for your message and for taking the time to post!
Updating the prebinding is not an obligatory task and should only be performed when you notice an inexplicable performance lag. As a general rule, performing it before and/or after system updates will not have an effect on the installation of this update, especially as most Apple installers do this for you at the end of the process (the task you see called "Optimizing".)
This being said, seeing error messages during an Update_Prebinding process should not, in itself, be cause for concern. Indeed, many files cannot be prebound for many reasons and your Mac is ready to handle that eventuality. The command is merely letting you know about what it encounters.
Once again, thanks for posting!