Me and my Mom have 03 Honda Accord EX's mine is standard hers is automatic. Her 2 front windows dont go down so I put my main switch in her car to see if that was the issue as to why hers arent rolling down. Now her key unlocks my doors, pops my trunk and will set my alarm all in unison with hers?????

 

The driver's door main switch has the door multiplex control unit (mcu) incorporated into that assembly. Since the remote transmitter was programmed in the the door mcu and you swapped it, the multiplex system on both cars are recognizing the same remote transmitter signals/commands.

If you reprogram one of the respective car's remote transmitter, it will no longer do what you're describing. See attachment.

Some fyi:

There are two types of programming.

1. Programming the remote transmitter for the door locks and window opening controls.

A DIYer can perform this type of programming.

2. Programming the key transponder chip for the Immobilizer system to start the car. Although the car may initially start with a properly cut key blank; if the Immobilizer system in the PCM does not receive the correct transponder signal, the engine's fuel system will be disabled shortly afterward.

A DIYer generally cannot perform the Immobilizer programming. Generally, this has to be done at the dealer and very limited number of specialized locksmiths with the proper programming software.

The transponder chip in embedded inside the gray colored valet key; which doesn't have any features to control door locks and opening the windows.

The transponder chip in a regular key is part of the remote innards.