They are almost bonus because I was thinking before that I would have to do something special just for the continental isthmuses. But actually, they are forming much the same way Central America formed, along a convergent tectonic boundary that is also astride 2 continental plates.
It will be pretty random though. Some games you might not have any, others you might have quite a few.
The player setting will likely allow you to alter the ratio between convergent and divergent boundaries. So more convergent would mean more isthmuses by default, assuming continents are next to each other.
I also just made it so that ocean-ocean plate boundaries are always divergent. It won’t make a difference right now, but there might be some uses for the distinction later on, and it generally fits the picture of a tectonic earth with all convergent boundaries including a continental plate.
And yeah, I am expecting the mountains to work out fairly well. I am figuring that they can mostly just form along the plate boundaries and then I can play with the Plains seeds to make them extend more or less into a continent. I can even do this on a per continent basis for a tight mountain formation such as South America, while also seeding a continent sprawling pile-up of rubble such as the Himalayas on another continent. Then put some erosion into them to both make them more natural, and round out some places for cities to settle. 
If it works out I won’t even have to seed hills. Seed the mountains, surround the ranges with hills, then erode everything down on some player controlled %.