Since I (apparently) can't fly from SAL to Choluteca, I was planning to drive. But then I had to think some more: Will I be required at the Honduran border or at the rental counter to show an international driving permit (IDP) or pay an extra fee for leaving the country with it? Or buy/show insurance beyond what I normally get from Allianz?
Expedia said Alamo would do my five days for $39. Added on CDW $55 from AIG, same price Allianz would do. After paying, they send me a document saying a cross-border permit must be purchased at the rental counter 72 hours in advance for $50. I'm supposed to sit in San Salvador for three days before I can actually make my trip? But really, it's $150: $100 for the privilege of crossing a border plus $50 for the permit. Finally, can't do it anyway unless you rent for seven days or more. Plus liability insurance which Alamo won't accept unless I buy it with their CDW (instead of AIG's) So, looks like buses are going to suck up half of my time in central America.
I have no personal experience, but from this Lonely Planet link from 2017 says that you can cross the border with your rental car, and that you get the permit when you rent it:
Renting a car in Guatemala was fairly easy. I used my American license and had to wait two hours for a car to free up since I didn't make a reservation. I also had to get a special border crossing permit to take the car out of the country (you are allowed to take rental cars to El Salvador, Honduras, and Nicaragua). The hardest part was going through the car check with the staff. It took us an hour to count all the scratches, dents, etc - this was no zipcar. The staff was very kind, and in the end I drove out of the renta autos with my cousin in the passenger seat and headed towards Antigua. I paid a total of $408.92 for five days.
However personally I'd take a bus. As you were already planning to fly its not as if you have planned to stop along the way.