the “external midi output” patch is just an example to get you started.
You can add midi output to each patch where you want to have external midi enabled: that means that you can combine anything.
Further is the teleport equiped with a switch: you can allways get the clean signal without iOS interference to your amp.
Sorry, I think I misunderstood your last post and replied accordingly. What Paul said is right — and he should know 
— Your clean guitar signal is still available for manipulation in MG2.