I'm always happy to help out! I'll answer your questions in reverse order, just to avoid anyone else seeing mega spoilers for the last one...
Question #3 - You can buy the bizarre fruit from Nathan on the Loican border (the verdant area in the southeastern part of Marema). He's hiding behind a tree on the hill to the right, and returning the bizarre fruit to Dan will lead into another "quest" (using the term loosely) depending on your progress in the story. Note that Nathan stops appearing in all of his normal haunts while he is locked up due to the events stemming from the "Lost Prototypes" quest; you will have to get him freed in order to make him start showing up again.
Question #2 - It is not possible to get into the observatory. Originally, there was going to be another Eloin quest there, but it tied in with the robotic characters (Willard and Kay), which were removed from the game in an earlier update; I plan to resolve the issue of the Steel Legion rebels in the next game in the series. Similarly, the bot fights in Battler's Dungeon were featured in an early version of the game (the player could actually fight all the way up to the Gold Championship level at one point), but were also scrapped; I may do a community discussion or devlog in the future to highlight everything that was cut out. Other than that, entering Loica, and resolving the pitched battle inside Oca Rongo, all other areas should be accessible at one point or another (but then again, it's been a few years since I started on this, so something may have slipped through haha).
In regards to a keycard, the only Key Items referred to as "keycards" that you should be able to get are:
A) The Pecasta Keycard (used to open up certain pathways into and out of VolTech HQ in Estancia)
B) The Level 2 Keycard (used to complete the 1st mission from Eight of Spades in Monolito Weapons Factory), and
C) The Kanolo Keycard (used to access restricted areas in the basement under the military base on Mateyo, which you can enter if you have Nyla in your party and have found a certain tool)
SPOILERS AHEAD
SO, on to your main question:
Yes, it is possible not to fight Vance and Ione; choosing not to do so will have an impact on the story moving forward (but will not change the eventual outcome) and will allow the player to get additional lore regarding many of the historical events involving The Destroyer. Generally, anytime Gregory was...less than open...about certain aspects of the story, you will get some additional info. Having Delphine in your party will give even more lore (with both the main and alternate paths). Additionally, choosing this path will give Nolan a different "passive" skill than the one he gets when choosing to attack. In order to unlock this "alternate" path, you will need to be rather thorough in your exploration prior to starting the quest, and try to gather a few of the "missing pieces" to Nolan's backstory.
HUGE
MEGA
SPOILERS
ARE
AHEAD
In order to unlock the "alternate path" you will need to do the following things:
1) In Accoro Village, enter the house in the top left corner of the village. Doing so for the first time will start a short cutscene with the man who lives there. (You can also check out the photo on the desk in the room with the twin beds for another little teaser, but it's not necessary). You do not have to do this "first" but it is necessary to get the alternate path.
2) Attempt to use the Trabunco Checkpoint Tunnel (the shortcut through the mountains on the western side of the continent) from either direction, and you will see a short exhange in which it is revealed that Nolan has lost his passport.
3) In Coluna's Old City (i.e. "fancy") district, go to the Vital Records Office; it's the small brick building in the center-right area of town. Talk to the man working at the counter, and you will receive a Passport (but not before Bridget gets the chance to make fun of Nolan for being so forgetful).
Now, once you have gotten back from your first trip to Mateyo and returned to Pedregal Springs, you should see the flashback sequence as normal; however, because you now have more of the facts ahead of time when you travel to the underground temple ruins, you will have the choice of whether to attack them or not! Again, make sure you have Delphine in your party, because she starts having more to say right off the bat if you choose this path...
ONE LAST LITTLE SPOILER
So glad to see people are actually taking Zaindari's words to heart!!! Incidentally, this is not the only "relevant" point of free will in the protagonists' journey...but I don't want to give EVERYTHING away just yet...oh, okay, just one...right after Butler's encounter with the Eloin, head back into the tunnel a second time. If you look to the right of the last staircase heading towards the sanctum, you will notice an alternate route that loops around to where you are headed. Taking that path instead of the main one will prevent the entrance to the sanctum from being locked, allowing you to access the chest inside. It contains Zaindari's Sword and Zaindari's Shield, both very nice items that Butler (as well as several other characters) would greatly benefit from. Unfortunately, once you've "locked" the sanctum door, it stays that way forever, so you may wanna check that out in a second playthrough... This is just a little one, but there are several other points in the game where certain choices will lead to better or worse rewards for the player...sometimes it's just a matter of looking around for that hidden path, object, or ally...