Yes, characters in GBE are generally worth more than characters in YBE. And the reasons for it are right there in your question: the world-transfer limitations.
This means that characters from GBE can be bought by any player, so the demand for them is higher. Characters from YBE are not useful for players who want to play on GBE, so only a portion of the player base is interested in them. Also, especially for characters with high level/skills, whenever a character on GBE is transferred to YBE it's permanently removed from the pool of characters of GBE worlds, which means that over time there will always be "good" characters migrating in only one direction.
It's a simple case of the law of supply and demand.
The actual differences between GBE and YBE are a lot less important nowadays. The gold once obtained through cheating has long been diluted by the amount of gold generated in places that have always been available in GBE servers. There's still some difference in regards to low level, high skilled characters offline trained for years, but this also becomes less and less important everyday as training with exercise weapons become cheaper and these characters are sold (and they can't be generated as quickly as they sold in the first couple years of bazaar).