We have no idea why Eonar may or may not have picked such a location. All we know is there is an infested World Tree there in the Nightmare version which has no explanation, and that Eonar once planted a tree somewhere that was ripped out of the ground long before any mortal civilization existed to remember such an event.
The devs don't always follow through on the most logical course of actions so applying our logic to something we don't know about yet can be a bit useless. By their own in-universe rules, C'thun's corpse being drenched in Azerite should have resurrected him the same way the watered down lifeblood of Azeroth in the Vale of Eternal Blossoms revilitized Y'Shaarj's heart, but so far we have yet to see C'thun again.
Planting the tree near C'thun is obviously a stupid idea since we know Old Gods corrupt the trees and the Dream through them (though the Titans couldn't actually know that yet since none had suffered that fate yet). But it being a terrible idea doesn't prevent Blizz from deciding to do it because they have a storyline in mind that requires it. Or if they want to utilize that Legion breadcrumb that they didn't think through when they came up with the idea.