I am amazed at the amount of information you are providing- thank you very much.
The assumption that the 2 Samuels' are the same has merit and your thoughts on the reason for the name change very valid.
With a purpose to either "divorce" his family or to possibly hide the convict past also has merit and it reminds me that years ago, when I first got hooked on family research, I was told by my grandfather (Samuel's grandson) that Samuel had married a Mary Montgomery at Windsor. It was only when I started obtaining all of the birth registrations for the children of this union, that I found out that her maiden name was McCrumb and later, that she had married a Charles Chuck (another convict) who died in 1854 and not too make it sound too far fetched, Charles came to Australia on the "Mangles" although in 1837!
When I questioned a late aunt about the name Montgomery, I was advised that it was to hide the convict shame of both parents being Irish convicts. The irony of this also is that her mother, Sally, left her father and took up with yet another convict, John Montgomery!
This is looking more promising as it goes- I have done a search of my DNA records but cannot immediately identify any Cohens although I did make contact some time ago with a DNA 2-3rd cousin who also had Jewish ancestry but he has not proven very reliable in keeping up the communication.