Can I cook 2 very different things at same time in the oven? I want to bake Chicken and Chocolate Chip Muffins in an overlapping time period, at the same temperature, in separate pans, of course.

I think it saves time, oven energy, and just is more convenient because both recipes happen to require the same temperature.

Is this ok / safe to do? Is it bad to bake meat with muffins?

Will the flavours meld wierdly?

Is there a certain arrangement the trays should be in?

Notes: 


The chicken is covered with tin foil with some holes forked through for steam. 
I don't think this is a duplicate because it's related to 2 different types of dishes. One is an meat dish, the other is Muffins - instead of 2 baked goods.
It is absolutely safe to do so...

For most foods, I would say that there is no reason not to.  If they are savory muffins like corn muffins to be served with the roast, I would not hesitate at all.

For sweet goods, with a high amount of butter or oil, there is some small risk of absorbing aromas.  I would generally segregating strongly aromatic foods for baked goods.  The foil should mitigate most of the possible transfer, but I wouldn't try it for the first time with guests.