I mounted mine inside my engine bay much like the pics from Carlisle. I found it to look very tacky and didn't even look good in my very not stock engine bay. This is just my personal opinion so if you guys that have it under the hood like it there then I say go for it. I just don't think I need to advertise that I have an MSD box by having that big 'ol thing under the hood. Some folks might think it looks cool and after all, spending a decent coin on it, they want to show it off.
I chose to drop my heater box under the dash and place it on the inside of the upper cowl. You can drill the hole through the cowl from the outside by taking off the cowl screen that cover the wiper arms. Have someone or something hold the box up from the inside and put the nuts on with a little sealer on top to create a moisture barrier.
Having it on the inside will further insulate it from moisture and heat.