I'd rather not see two distinct methods of doing flight models in outerra as it very rapidly polarises the community and that's a very bad thing.
It wouldn't be two distinct methods...it would be numerous methods, because it would depend upon the developer as to how they chose to do it.
If you want to use JSBSim, then do that! There is no point limiting the sim to "only" JSBSim, or any other method, because of a perceived "split" that might arise.
It makes no sense to limit what is possible based upon someone's biases towards a particular method. It should be open so anyone can use any method they like (within certain technical constraints). If you're not careful, you get into the trap that numerous simulators of the past have faced - that they force the developer to using one method, and as a direct consequence limit what developers are able to do.
That visualisation tool could be used for JSBsim and would make flight modelling easier, producing more accurate flight models
Yes, and not only JSBSim, but other techniques as well. As SE explained elsewhere, the visualizer only uses JSBSim for integration methods (essentially, to emulate the missing half of the simulator) so the flight model code can run complete for analysis; it doesn't have constraints as to how the flight model is computed - it doesn't know or care if you use XYZ method or JSBSim for the calculations.