Are you limited to the options in the Custom Table setup or can you add other items perhaps through Syntax? I need it to compare column proportions for "computed categories" and compare the column mean scores, showing the A/B/C letters to indicate sig diffs for both of these. Is this even possible?

That's an interesting question to me, since I have just completed a project where I had to add the significant difference letters taken from GLM multiple comparisons output into a table from CTABLES. This required heavy use of Python programmability and OMS..

However, you can extend what is contained in a CTABLES table or, in fact, any pivot table with the STATS TABLE CALC extension command. It can add or replace rows or columns in a pivot table with calculations based on the data in the table or even from another table. Simple calculations can be done without any knowledge of Python; more complicated things would require Python knowledge.

You can install STATS TABLE CALC via the Extensions > Extension Hub menu. It has a dialog box with help, and syntax help is also available.

You can, of course use the Python programmability functions directly to manipulate tables and other output.