The destroyed Leopardon being rebuilt and upgraded makes perfect sense when you think of Tokusatsu and Super Robots: how often is a hero's mecha wrecked but reconstructed to better fight the new villain?
Also, Considering that Leopardon's original suit was stolen, Marvel actually finally gave it the Mid-Season Upgrade it could never get!
Well no other spider hero on Earth 13 has a problem with gathering in the clearing, the Earth 616 Peter is nervous. This actually makes sense when you remember that 616 Peter also once had the Enigma Force, and lost it. He knows that it can be beaten, so he wants to be in a safer location in case it is. And if you think about it, he's right. If they were in the city, than once the Earth 13 Peter dies, most of the Spiders could run away from the inheritors. Well they are not as strong, they are faster than the inheritors well web swinging, something that they cannot do without tall objects to swing from. If they were in the city, no where near as many spiders would have died before they could escape, and they would not have had to sacrifice Leopardon.
Fridge Logic:
In the Epilogue issue, Karn mentions that the reason why Peter and Otto, who are from the same universe, can be on Loomworld (Earth-001) simultaneously is because of special physics of that world that allow for manipulation of reality to that degree. However, they also crossed paths on Earth-13 in issues 10 and 11 of "Amazing Spider-Man", which did not have any of those changes.
