OK, I don't know if this helps or stirs the pot more.... I found this on Surge Protector - Only for Shore Power, or on everything?? - iRV2 Forums
What he's saying seems to make sense to me.
"It seems most people put it before the transfer switch. That's what Progressive recommends. They say it's to protect the transfer switch, and it's not necessary to put it after, because the generator is a cleaner source of power with its own protection.
But I don't buy that logic. A transfer switch is basically a set of relay contacts. There's nothing there that is easily damaged by the kinds of things the EMS protects against: high/low voltage, surges, or wiring problems. The odds of the incoming shore power damaging the transfer switch are VERY low, and if the worst should happen, a transfer switch is one or two hundred dollars, tops.
On the other hand, generators can fail, and when they do they can cause all sorts of nasty problems, including very high voltages if the voltage regulator fails. If that happens, the potential cost to equipment in the coach could be in the thousands.
While I've heard of transfer switch failures caused by loose connections or switching while under heavy load, I've not heard of a single transfer switch failure that was caused by bad shore power. However, I've heard several stories of massive coach equipment damage caused by a failed generator.
So, would you rather risk an inexpensive piece of equipment that is robust and not prone to failure, or would you rather risk many expensive pieces of equipment that are more likely to be damaged? In my mind, the decision is easy: don't worry about the transfer switch, but protect everything else from shore power AND the generator -- I put the EMS after the transfer switch."