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The more I look at it the more I think it was an accident. Venomoth is really close to Caterpie and Metapod but this was also at a time when they were completing evolution lines by introducing evolutions to much earlier standalone designs, hence the Butterfree being there to complete the Venonat line.
It just so happened that it got in right after Caterpie and Metapod so to whoever was in charge of programming pokemon evolving into eachother saw a larva/cocoon/butterfly in order and understandably did its thing by mistake and the rest is history, though it wouldn't surprise me that they picked up on the blooper and just didn't care enough or thought it was cool to keep it like that.
