An example of what you are talking about would help.
Assuming it really is an engraved stamp, the transfer cylinder would not be normally reworked, but the master die. The master die would not have cut marks or alignment marks, but those would be placed there during the making of the printing plate.
Typically, one stamp of a single color and integral design (meaning the whole design is engraved at once, rather than a frame, vignette, value markers, etc.) is a master die.
The transfer roller is made with a single image
The transfer roller is then used to place that single image on the printing plate, multiple times, in proper place to make up a plate.
Any additional marks can then be added to the plate (Like plate number, alignment marks)
Here is a printing plate for a Cuban Airmail stamps, the color red element.
The master die would be a single engraving, transferred to the transfer cylinder, then rolled out 8 times to make a single plate.
You can repeat the process many times to create as many plates as you want. Any changes, either rework the plate, or, the master die.
