Tested this...
I start off bringing in 3 Magic per turn.
When I set my L1 City to Produce magic, I bring in 4 magic Per Turn (no Claimed Shards).
Once that city reaches L7 (still Producing Magic w/ no Shards), I bring in 10 Magic per turn.
Seems to be working to me
But let me know if you have a save game or a repro case where the proper bonus isn't being given.