always flatten in converting ReactionSystems to other types

It would have no impact on single systems, but I think it would avoid https://github.com/SciML/ModelingToolkit.jl/issues/1274

This change, along with https://github.com/SciML/Catalyst.jl/pull/427 should finish off everything we need for basic compositional modeling, and we would be in good shape to make a new major release. 