The friendly sync in the ignition is tied in with the passive immobiliser. If that has been turned off in the BECM, then the key won't sync in the ignition, and HAS to be done in the door.
The vehicle worked exactly as it was designed to. If you lock the vehicle with the remote, and unlock with the key, then you WILL need to enter the EKA (either via door lock or Nanocom if the vehicle supports it - IE BECM PAM V36 or above - which from memory is mid-97 onwards).
As far as I can tell, the idea behind it is that in the days where you had a valet key - you could leave the vehicle with the valet at your country club, give him a manual key and keep the remote fob. They could then start and drive it to park, lock with key in the door. They could then unlock with key in the door, start the vehicle and bring it back to you. Now, if they'd decided to copy your manual key and then wanted to try and nick the vehicle - assuming you had locked with the remote (which LR tell you to always do in the handbook) - they'd turn up and unlock the drivers door with the key blade - but then no be able to start the vehicle and drive it off... The EKA is there as a backup to the remote not working - so if you had locked with the remote, but then it stopped working for any reason, you could then enter the EKA code in the door to get the vehicle mobilised and moving.
So if your fob has stopped working, and you'd locked with the remote - then you only being able to open the drivers door is totally normal. Entering the EKA fixed that and got you moving. If the key isn't resyncing in the ignition, then try locking it with the key in the door and pressing the lock button on the fob, and then unlock whilst pressing unlock button. It should resync the key that way.
I don't know if your BECM has passive immobilisation turned off or not. But as I mentioned - along with turning off the feature where the vehicle will automatically re-immobilise itself after about 30s of inactivity and the key out of the ignition, it also turns off the friendly sync in the ignition.
Hope this helps clear up how it works, and why your vehicle did what it did... perfectly normal.