With all due respect, don't do everything what Apollo recommends ;)
First, everybody in Amiga world expects Kickstart to be the original one. By modifying it you are just creating unnecessary problems for yourself (and this thread is just a proof of that).
Second, the intuition.library 45 is not the only library loaded by LoadModule in AmiKit with OS3.1.4. It also loads icon.library on startup. That means that even if you inject the intuition library to ROM, the LoadModule will still be used for icon.library.
If you really insist on using such modified and unofficial ROM, edit S:Startup-LoadModule script in AmiKit and remove the "intuition.library" part from the OS3.1.4 line, but keep the icon.library there. Just be advised that if a new AmiKit update arrives, it might overwrite the Startup-LoadModule script.