The shop is meant to add longevity to the server. If you can only make things out of cobble and wood (and stone variants from cobble) then the game would get boring quite fast. Not to mention it would be stupid hard to get your island up to level 1000 and most likely everyone will leave before they get to that point.
And no one is forcing you to use the shop anyway <object class="emojione" data="
https://resources.enjin.com/1489581540/themes/core/images/emojione/svg/1f61b.svg?0" type="image/svg+xml" standby=":p">:p</object>
Spawning on top of the tree is a issue with the way the plugin generates the island and is outside of my control. You can move your island spawn with the command: /island sethome