I liked being able to just straight replace the image in Tiled and have everything still matching. But really, given the nature of this, I'd say go with whatever is easiest for you!
Moving forward with this set, I have a quick question about how to update with new variants. Would it be better for people using the set if they were just appended to the main tile set image so that image would keep increasing in size? Or would you prefer it be a separate image that is just that theme or variant?
Respond to this or participate in the attached twitter poll if you have an opinion, thanks everyone! I'm still super pumped that this set is at all popular and I hope you're making awesome things with it!