Actually, the game on the left uses roms while the game on the right uses a rom and an eprom. Yes there are eproms without windows, but these are not them.
Unlicensed game companies did not have to follow Nintendo Standards, and therefore there were a lot of hokey things that they did with their boards. I've seen many different internal configurations for the same unlicensed game.
You might dump the games and see if there's any differences. It's quite possible that the game on the eprom fixes mistakes from the rom version, but they didn't want to actually get more roms made. Roms are cheaper if you need 10,000 roms. If you only need a couple hundred, it's much cheaper to use eproms...

It's not going to be worth any more for the same retail game, especially since there are so many internal configurations for unlicensed games. There are even different configurations inside some licensed games, but I've never seen it change the value of the game. (The earliest Bases loaded even has an extra chip to fix a problem with the rom--kinda cool but not worth money)