For all these collectibles related trophies:
*1)
as well as
*1) diRavello's story will alway be told in chronological order, independent from the pick-up location and -order
If you completely liberate a region, it's collectibles will get marked (in that specific region) with a "?" on your map.
Or you can use this interactive map from IGN.com to collect them from the start.
http://www.ign.com/maps/just-cause-3/mediciBut I would recommend playing at least the 4th or 5th story mission, so that you are able to perform quick travel and have 1 helicopter unlocked in your rebel drop supply list. Furthermore, the "Cauda" region in the south-west corner of the map, is the rebels hideout and liberated from the start. There, you can find a jet as well as planes on the airstrip.
As always: Please leave a comment or suggestions if you think somethink could be added or is unclear. Anonymus downvotes of solutions are not fair to the author.