You can configure a serial number via rtl_eeprom, but I think you are going to run into the problem that the kernel DVB-T driver will want to grab all devices with a particular USB ID regardless of serial number.
I think there is some kernel-level SDR mode in the driver now which might coexist better, but I have no experience with it and it would probably need a bunch of integration to get working with things that are expecting the userspace librtlsdr.