I say render the midi parts as audio as soon as the writing, performance, and sound or patch is final. Just like when you would record guitar or drums. At that point, you have written the material, decided on the sound you want, and when you record it you're going to keep the performances that sound good. With midi, you've "recorded" the performance first, and are free to change the sound or the writing / performance later. So as soon it's all as final as it's going to get, render it. No point in holding onto it. So render it and it becomes another track to be mixed like the others.