I doubt the new system will be deliberately incompatible with MRT transponders, but at the same time it wouldn't surprise me if it was accidentally incompatible.
By that I mean that when doing backwards compatibility tests Mylaps never actually tried with an MRT transponder to see if it works or not. However, since they are functionally identical to the old AMB's as far as the loop/decoder goes I can't see how that can happen.
What sounds more likely is that with the new numbering system Mylaps will need a better track of who owns which numbers (so you can have xxxxxxx1 in one car and xxxxxxx2 in another) and maybe make a big central database. All those MRT's floating around with non-original numbers might cause some issues there as you'll get several people (worldwide) with the same 'unique' number.
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Yz4 - Yz2
DEX210 - Cobra 4210- DEX410
RC10 Team - Manta Ray - RC10T
Mini Trophy - Blizzard - Wheely King
Tz4 - GT24B
BMRCC
Emergency back-up race controller
(but only if nobody better is available)
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