Curious, car will not enable alarm with the key in the ignition and manually locking the door. However it will enable the alarm with a key sitting on the console and manually locking the door. So it seems the key is only recognized by the coil in the ignition switch itself.
Unless you've keyless start, this is how it should work anyway. The immobilizer system, which recognizes they key (well, actually an RFID chip in it), and the alarm system, which is controlled by the buttons on the fob, are two separate systems, that work independently of each other. The only connection and interaction between them is that when you disengage the immobilizer that also disarms the alarm system, even if it not has been disarmed through the remote controller.
And if you don't have keyless start, putting/leaving the key on the center console shouldn't do anything, even if everything works normally, because the car just wouldn't even know it's there. It can only sense the immobilizer chip when the key is inserted into the ignition lock.
I think we can rule out a hardware antenna issue. Keys worked fine prior to all of this and had good range.
Did you try putting back the removed fuses whether it solves the problem with the alarm?
01299 - Diagnostic Interface for Data Bus (J533) 005 - No or Incorrect Basic Setting / Adaptation - Intermittent Freeze Frame: Fault Status: 00100101 Fault Priority: 3 Fault Frequency: 14
This might be related to the radio unit (or other units possibly powered by the same fuse) not working now. Btw is it the original factory unit that the car was built with? And I'm not asking whether it's an oem unit, but whether it's what the car was built with. Can't it be that it's an upgraded unit that's CAN-bus 2.0 and is using a converter kit?