the 0.12a version of vt+ has already included support for giving modded characters custom ids, though I'm not sure if your version is different or not as the vt+ ids are in fact hardcoded
I have not had the opportunity to work with anything 0.12a related yet, so I do not know of the new VT+. The current thing I have in place just checks for an [ID] tag in the Class file when loading the mod. If an [ID] tag is not included then an ID is added as normal. 
Could not find a way to ensure that modded units would always have the same ID independent of load order, which they would need for the "Summon" skill to work, so I use this for testing.