I don't think android would affect the IMEI that gets sent to the network, and the intent of the law was to allow tracking of phones by IMEI (kinda scary in itself, kinda useful for law enforcement) and to allow stolen phones to be blocked from the network and rendered useless, which AFAICT has had a huge impact on levels of phone theft.
>> But a person does not commit an offence under this section if—
>> (a)he is the manufacturer of the device, or
>> (b)he does the act mentioned in subsection (1) with the written consent of the manufacturer of the device.
Perhaps the manual that comes with your phone could come with a line in the license saying that modifying the IDs for the purposes of stopping apps snaffling data is allowed.