Based upon the experience I just had with modding in the vbAdvanced CMS Portal I would have to say that it depends on the complexity of the mod.
The vbAdvanced CMS is easy enough to install (I think it took about an hour to go from no domain, to domain, to vBulletin, to vbAdvanced.) This one can be copy pasted without too much trouble. There's a few files you'll have to rename/restore before you do it and those will be obvious.
I don't see any reason for the direct copy to not work in most cases. I suppose a dry-test on a dumb-domain ahead of time would be a safe bet just to make sure you had the method correct.
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