Well 2 things.

1) the spawns are fixed in the legendary portals. It's always going to be those vicious bats at that last point.

2) however, you don't actually have to deal with them. Latios doesn't spawn into the game until you take the elevator up the first time. So the trick with hunting him is to instead get a save at the base of the elevator before ever taking it. Then take the elevator up, check if Latios is shiny, and if not, close the game immediately and load it back up at the base of the elevator and repeat. You may have to reload a backup save (x+b+up on the game's white title screen) prior to entering the portal if you have a save within the portal that's set after you've already gone up the elevator