It's actually a stop for you. The LAX-GUA is flight operated by Avianca Costa Rica on AV641 which stops for fuel in GUA. Your second flight is operated by TACA (Avianca El Salvador).
Bags go to SAL directly, no customs in GUA. Same as SAL, you probably walk next door to the next gate.
The inbound LAX-GUA is a good flight, you get an amazing view of GUA on approach while the sun is coming up and the volcanoes look nea.t