The official patches patch the official mods (at least, the ones that get patched). There are even usually separate sections in the patch notes for each mod that was specifically patched, although this is not be the case for 3.19 (3.13 had a specific Nest War section), and they pick up any relevant changes for the base BtS files like the changes to the DLL (I think the only mod that comes with BtS that uses a custom DLL is Rhye's and Fall of Civilization, although I'm not sure of that).
They also patch, effectively, all the other "unoffical" mods too, although the extent varies. Any mod that uses a custom DLL will not get the DLL changes in the patch (unless the mod is updated to match) and may actually break (since the EXE may require some of the changes done to the DLL, it checks the version). Any XML file that the mod replaces won't get the changes in the patch (unless mod is updated). Any Python files that the mod replaces won't get the changes in the patch (unless updated - see a pattern here?).
td;dr : The official patches keep the official mods up to date. It does not break them.