Just reading this again, and I thought this bit was odd too, particularly about the boot (assuming I'm reading it correctly).
So none of the keys will manually unlock the boot ? Or are you just referring to the remote opening of the boot via the key button ? I've never tried it (I'll have to check) but I presume that the "sub" (valet) keys don't physically work on the boot, just like they don't work on the glovebox. If that's the case then that sounds like you don't have a master key, which will be another problem because you won't be able to program keys yourself (e.g. to make the remote locking/unlocking work), without the help of an auto locksmith or Toyota/Lexus.
As I said I need to check this on my own car though, unless someone else beats me to it with the facts on this.