I'd probably go further than that.
I always save off my RenPy folders to a separate drive in case something gets borked on my laptop, or in case I accidentally save over something I didn't want to - I always have a second source to go back and grab an clean save. This has saved me more than once, especially after I had to do Sancho gymnastics on a few VNs when he disappeared.
In this case (if I were to do the Steam, which I haven't), I'd save the Steam in one folder, along with the Steam RenPy folder with persistent and save files specific to the Steam version in one set of folders on the external, while I saved the non-Steam version and non-Steam RenPy folder, with the specific persistent and saves for that version, in a separate folder. Then, if I wanted to play one of them, I'd pull the appropriate version along with the appropriate RenPy folder over to my laptop/pc and play it there. The reason is that I would think the old version saves wouldn't be consistent with Steam and vice-versa. Maybe you could put all the saves of one vesion on pages 1-10 (or whatever) and all the saves of the other version on 11-20, and then just move the persistent, but that could get even more confusing.
Now, the Dev might be able to prevent issues if they were to create a differently named RenPy folder that gets set up when you install the Steam version - I had a couple of VNs do something like this when they went from "book 1" to "book 2" and upgraded engines - the old "book 1" stayed separate, "book 2" ported the "end of book 1" save data, and started a new persistent for book 2 in a separate, but similarly named, folder.
Any way you cut it, if you cross contaminate you'll probably end up with fucked up saves and cry a lot (then have to do speed runs skipping unseen text).
