How can I make a custom content entity ID editable on the content entity form?
You have both a widget configured and a custom form element, that results in Drupal being confused about the structure.

If you have a form element defined by yourself, don't define form display options and you should be OK.

The reason the widget show up like with other fields is likely actually a regression with the security fix in 8.3.1 that denies edit access to the entity. When we did that, we didn't anticipate a use case like this. You could override the default fieldAccess() method on the EntityAccessControlHandler to grant edit access to the id field, at least when it is new.

Or you do not make the lot number the actual entity ID but have a technical auto-increment ID, then you don't have to worry about this stuff.