The only explanation I can come up with in relation to fuel transfer is more of an arse-covering measure by Beechcraft.
You can have up to a 1000lb fuel imbalance per side (wing lockers will reduce this figure, something like 700lbs imbalance?), so a few hundred pounds imbalance whilst all engines operating is no big deal. I've previously flown one about 400lbs out of balance. Nothing drastic.
Unless you/someone else are incompetent in refuelling you are never going to be in a situation getting close to being out of balance.
I highly suspect the system wasn't designed to transfer fuel, um, "normally" but rather designed solely for the one-inop scenario, so my best guess is that they just tell you it's a limitation.
On a similar fuel topic, here's a fun thing to think about.
Why must the main tanks be full before putting fuel into the aux tanks? It is another unexplained limitation from the books.
Think about how the fuel system works. Can you remember it???
This is what I've come up with - keep in mind its just my theory!
It's all to do with the motive flow. One needs fuel in the mains (and fuel in the aux to open up the motive flow valve) to be sent through the jet pump in the aux tank- the jet pump is just a venturi. This fuel which has originated in the main tank flowing thru the jet pump creates motive flow and thus "sucks" fuel from the aux tank.
You will obviously need a certain minimum amount of fuel in the main tank to be able to provide enough motive flow and draw out a full tank of aux fuel- so far I have not been able to determine just how much though.
One way to think about this is in the extreme. Fill up your auxies and leave the mains empty. You aint going anywhere! The auxies do not supply fuel to the FCU "directly", you need main tank fuel to provide the motive flow.