When a table appears in an Enterprise Guide project, it is marked (Read Only). This has always been a desired performance for me, and the people I have tutored through using the product since Version 2.
An important aspect of this behaviour was that one could not delete or damage external tables through the EG Project. This was especially important when the right click menu on a table included "Delete", which was not really "Delete", but was actually "Remove".
On the face of the project, the table is selected from a library, or created from one or more steps. If it were possible to run a step, create a table, and then modify the table through a manual and untracked process, then the project would be anomalous.
I can't find any back door to turn off the read only flagging on the table, indeed I hope no such back door exists, and until that is turned off, you won't be able to modify the structure or content of the table.
If the developers add a task called "Manual table update" that one could select which produced an output table containing your changes, then that might be helpful. Perhaps, some form of table designer as is available in Foundation SAS.