It will depend on the rental car company but in my experience there are no drawbacks to what you are suggesting, I have returned a car plenty of times much earlier than expected on the same day and never faced any penalties.
This happens and sometimes the different is significant. Without knowing exactly where you reserved and the pricing details, we cannot tell what computation was used but it's only a result of pricing structure.
A weekly rate is almost always cheaper than 7 times the daily rate, so when exceeding 6 days, even by a few hours, you get charged as a 7 day rental ...
As you have said before, I think there is no problem when crossing with a car rented from Salvador to Honduras. I was seeing some information in this website and apparently if it can be done ..
I hope I've helped
I am Salvadorian