No basic rule, no. In your above case, for example, you cannot encounter a Baby Ape
outside of its unique spawning conditions. They can only
appears on Jaguero Isle when it rains. I don't know if the Ape appears as a secondary pet at all, though, even in those conditions.
Other pets can appear throughout the zone as secondaries. The Snowshoe Hare
demonstrate this behavior. They do boast their own spawns, but can also be encountered as an additional pet in any battle in the zone. Additionally, there are instances where this can bypass a pet's special spawning conditions: Though the Widow Spiderling
only spawns at night, it can be encountered as a secondary pet in Duskwood at any time of the day.
There are also numerous instances where a pet can only appear as a secondary within the region that it normally spawns. Several of the zone-unique Outland spawns, such as the Flayer Youngling
and the Scalded Basilisk Hatchling
function in this manner.
Ultimately, the circumstances around each pet can vary dramatically. If you are seeking a pet in particular and not having much luck, do a little research and return to your task when you better understand how the specific pet functions.