The Bonus quest line launches once you take Garrington and Las Penas. Scouting Garrington does not launch the Bonus Quest line. Taking Las Penas alone does not launch the Bonus quest line.
To that, I'd add that I only triggered the Indy bonus quests when I acquired the last sector of Las Penas, which was the only province I hadn't acquired. Since Garrincton gives an expansion, I figured it was better to acquire Garrincton, and leave Las Penas alone.
There's a complication, though, if you want to complete the Indy story quests. There's a 4-way choice to make - whether to fight against the North, fight against the South, fight against both, or fight against neither. I think some choices might require you to take Las Penas, and some choices give different types of Indy unattached units, or different amounts of diamonds. I fought against the North, and negotiated with the South, and made it all the way through to the PE story quests, without having to take Las Penas. My notes are fuzzy on the details, but in the end I decided that fighting against the North would give me the best combination of good unattached Indy units, and "not having to take Las Penas". If you make a different choice, let us know how it turns out?
(There's also a choice about whether to fight or negotiate the first province, but that doesn't matter here. Although I think negotiating eventually gives a few more diamonds than fighting.)
I gotta say, though, that I did not enjoy fighting in Indy, even with units from PE and ME and PME. PE was much more fun. And if you don't plan on camping out in Indy for a long time, then you don't need to worry too much about avoiding the Indy bonus quest line. Just don't forget to save a cultural tech (like Indy "Infrastructure") for the 8th quest of the Indy bonus quest line (""Enemy Propaganda"). And maybe try to pick up 2 Indy "Police Station" buildings from GE or daily quests or something. There's a PE story quest ("The Peace Conference") that requires building 2 Police Stations, and if you have 2 in inventory, you don't ever need to research the Indy "Law and Order" tech (which unlocks Police Stations).
