I don't think it would be a hassle, I think it would be the best solution.
Say you want to make an explosion plugin for HTML5, you click it makes an explosion effect. If you made an explosion plugin that was 1-fit-all for all exporters, you wouldn't be able to easily make best use of all that platforms unique features. It would probably also run a lot slower overall on all platforms. It would be incredibly different to maintain.
So it's better for the Javascript expert to make the explosion plugin, then the DirectX expert to make a different explosion plugin.