The set back is, insomniax and caffeine don't shut down the display when you close the lid.
In order to counteract this, setup a hot corner to put the display to sleep, and use that before closing lid.
The problem with these programmes, is that it is easy to forget your Mac is awake, and this is where the overheating problem can come into play.... be it on and closed for very extended periods, or put in a bag, case, etc in this mode.
As you will notice, parts of the upper keyboard and surrounds get very warm, and therefore, being in clamshell mode with or without these apps is not going to allow this heat to dissipate.
Everyone will have opinions on the above and more... I have just merely stated some facts that I am aware of.
Even though very minimal, and it varies depending on the model of Mac notebook, I believe that there is little airflow around the keys, which is prevented in clamshell mode, etc.