Taking your suggestions in order:
1. Related Element heading levels: I fixed this in 3.4
2. Extra spaces after tables. This is needed just in case the next thing to get printed is also a table, in which case Word will assume they are the same table and join them together. This is probably the longest-running eaDocX issue, and I look at it again for each release, and each time I try to remove the space, lots of other test cases fail horribly.
3. Have you tried switching Compact Document to FALSE?
4. What’s the formatting from ‘System Function’ to ‘System Element Functions’? Rel. element, or simple relationship attribute ?
