Will,
Others may go into more detail, but for starters:
Wings create downwash when they create lift. The flow off the TE aims 'down' compared to the direction of lift aiming 'up.'
Theoretically, then, a 0-0-0 layout has the downwash miss the horizontal tail. But, consider: stunters have enormous lifting capacity for their weight, so in level flight, straight tracks, and even round figures, the downwash does not make an extreme angle coming off the TE, and it smooths back as it moves aft of the wing TE...
Also, the 'masses' (weights considered in view of their momentum/inertia) of wing, fuselage and tail being in line, there should be a more equal ability to turn both ways. However, with thrust line on wing and tail chordline, only a sidewinder engine mount, and no landing gear - or retracts - keeps those masses "centered" in that sense.
The "normal" layout: inverted engine, thrustline above wing chordline and below stab/elev chordline, works well. Personal opinion - 0-0-0 full stunters look a bit odd, IMO not as attractive as we can do with the "normal" layout. 0-0-0 looks sort of scrunched up, like a guy ducking his head into his shoulders... IMO.
0-0-0 fuselages may create some interesting complications for engine and tank installation, control linkage routing, and landing gear.
The "normal" layout allows a shorter landing gear, usually, which looks better inverted than a pair of stilts reaching upwards...
With the longer control horns we use these days, there may be problems keeping them indoors at the back end with 0-0-0. Also, raising the wing chordline can make the slope of the pushrod from flap to elevator much more severe. That DOES have an effect on neutral and rate of angle change at the elev. A 'cobra' type flap-to-elev horn becomes more crucial.
NEXT?