Absolutely,
This is one of the features on my list that I want to add.

I am aware that many 'PCBers' use different offsets for top and bottom, but personally I have never tried anything other than G54. If the original file is G55 for example then the additions made by Autoleveller should not affect this and G55 should be used in the output file as well but I haven't tested yet so I cannot confirm. It might be best to stick with G54 for everything currently. As you say though there should be an option to explicitly set the offset.

thanks,