I've used old CD cases that only held a few CDs. These also hold the battery pack, paddles (have both the Whiterook paddles as well as the Palm paddles and a few straight keys), antenna (LNR TFR 10-20-40 or dipoles), earbuds, string and any other accessories, as well as the MTR3. The hard plastic that kept the CDs neatly aligned provides protection in the cloth cover, and a few zip lock bags go in if needed for rain. The radio gets bubble wrapped. Need to build a 30m antenna, but already had the TFR. XYL doesn't even notice the small radio pack in the truck.
Same case also works for my DSW-20 and SST-40 with the usual accessories. Both radios go in the kit at the same time and share accessories.
Disused small digital camera cases are also padded well, and found one that looks to fit the MTR3. Maybe even try one for the radio and one for the accessories. Sometimes easier to pack two smaller bags than a slightly larger single bag into the backpack.
Usually find these used camera bags and CD carriers at thrift shops and second hand stores. Cheaper that way. Now just need to find more time to get out and on the air more and use these goodies. Pass on what you find to work, always looking for new ideas.