No matter the size, generating a chunk is going to take more resources than loading one from a file, so at that point it's an issue of whether you want to prioritize keeping file size low or performance high. Personally, for a game like this, I think performance is the top priority, especially on a server. However, a config setting for that could be useful for some people in single player, as long as it isn't to costly to implement. Adding a check for a config flag adds to processing time, even a small amount. I don't think a once-per-chunk check on generation would be noticeable, but as @7embre pointed out, on large servers everything gets magnified. That also includes file sizes, of course, which could get absolutely insane with many people using translocators to explore, so some way to cull unmodified chunks that haven't been loaded in a long time from the save could be needed.