The thing about an isolation transformer is that depending on exactly what and why you are using in there are at least 4 or 5 different things that can make sense to do with the earthing, and some of these will not make working on a live chassis safe!
You can:
- leave the output connector earth off entirely
- Carry the input side earth thru to the output connector but leave the secondary floating
- Earth one side of the secondary from the input earth, with or without carrying the earth thru to the output connector
- Connect the output connector earth pin to one side of the secondary, but leave it isolated from the input earth
- Connect the input earth to the secondary centre tap
And this list is by no means exhaustive.
All of these are useful in specific situations, and all of them are potentially lethal in other situations, you really cannot talk about an isolation transformer making something safe without going into a lot of detail about what exactly you mean by an isolating transformer, what the load is and what you are trying to protect against.
RCD (GFI) protection does not carry across a transformer for obvious reasons, and in the case of one where the secondary has a terminal connected to some sort of ground, you need to think about exactly in what order things hook up.
Now personally I am of the view that the actual need for an isolating transformer should come up so seldom unless you are hacking switched mode power supply designs that I personally don't even own one, if you need one often and are not a hardcore power engineer you are probably doing something wrong.
Stay safe all.
Regards, Dan.