I won't deny there are slight spawn contradictions, as not everything within PWO is accurate to the official games. However, by taking these things into consideration, we are doing a sort of quality control.
Yes, you're right in that we could add any spawn we wanted into the game. But you wouldn't throw a pidgey into the middle of an ocean, would you? It's the same concept. We can't always do weird stuff because it's what players want, not that we don't take their wishes into consideration. We didn't just take out Trapinch and go "Lol sorry guys no cool rewards for you. Cause we suck. We didn't put anything you wanted into the den." We instead compromised and added Bagon, something that was arguably even more coveted.
Trapinch made no sense, Bagon did. Sorry that there was disappointment with this change. Honestly it should've just started with BAGON right from the beginning so that people wouldn't get their hopes up. However, it didn't, and the weird environmental matchup was corrected later. In fact, I think it was changed before many (IF any) even had access to the area.
In summary:
Just because people want trapinch doesn't mean we can just throw him into random areas. It's about quality and consideration; creating a world in which you can submerse yourselves as effectively and easily as possible. How can you do that when the spawns contradict themselves constantly? You could possibly get away with that/use that effectively in a new world or concept, but this one is well established. We shouldn't just go "Lol screw the well thought out, original, and professional designs of the franchise" just because people want a certain spawn. :L
And sorry if I seem rude, I'm just wording stuff as efficiently as I can. XD Debating is in my blood.