Technically there are no restrictions on any of the TOC marker contents except that you cannot have the book names the same for two different books. The most common issue is the abbreviations for books that have similar names like John and Jonah, and Philippians and Philemon.
Another issue is if you put the number for John’s epistles after the name you can end up with reference errors. For example like this:
JHN \toc2 John
1JN \toc2 John 1
2JN \toc2 John 2
3JN \toc2 John 3
With these
\r John 1:1-15
will create a reference error.
My solution is to put a no-break space in the Johannine epistle names:
1JN \toc2 John~1
2JN \toc2 John~2
3JN \toc2 John~3
That said, you need to know how you want to use these different ways of referencing books. If you are creating center column cross-references you need very short \toc3 abbreviations. But if you only want cross-references in footnotes you can use whatever you want. You can even make \toc1 \toc2 and \toc3 the same and Paratext will not complain.