In the new builds, could someone change the save directory? These saves aren't really compatible with the core game anymore, so using a separate save directory would be best. It's not a big deal for people who only use one or the other, but someone who uses both has to keep track in their heads of which saves belong to which version.
This can be done by changing the config.save_directory (line 304 of options.rpy in the game folder of version 0.980) to a new value, such as "Rogue-LikeX". There's a few other properties in there that you could change if you wanted to differentiate more, but that would at least split the save directories.