I have yet to see silver, gold, titanium, or gems. A lot of fossils and tech fragments, coal, copper, some iron here and there. That is about it. Maybe we could trade some resources? I would like to have some stacks of better materials so I don’t have to worry about using my precious metals that aren’t precious on other worlds 
Just my two cents:
The tree thing is realistic. Why not make the tree fall over onto the ground when you chop the base? It avoids floating trees and maintains the need to cut the tree with a tool, but it is now on ground level. Therefore you don’t need a dirt tower.
I completely agree with world regeneration. Natural world regeneration, a living environment.
Trees
Shrubbery
Grass
Edible forage
Other plants
Holes filling in
Animal populations
All of the above should regenerate relatively quickly.
Ore
Stone
Gems
Fossils
Fossil fuel
All of the above should be regenerated relatively slowly, and in different spots.
Buildings
Ruins
Abandoned buildings should decay over time. Wooden and thatch ones faster, stone taking in-game years. Even centuries, realistically. I’m unaware of time flow in Boundless, however I was part of a town over 300 minecraft years old. Overgrowth and such could be a feature.
Ruins of ancient times should hold rare artifacts and resources that can’t be replicated. The rarer the resources, the longer they should take to regenerate, based on an overall world limit. With some, like ruins, not regenerating.
As far as inflation / deflation /resource abundance are concerned, it is a genuine concern. Runescapes economy was devistated by rapid devaluation of almost everything due to rapid increase of supply. I kept most of my assets in gold coin because of that.
Artificial methods of economic control pose a danger to the free market. An indirect way of helping maintain a degree of stability would be changing spawn rates of certain materials, therefore adjusting the supply chain.
In games like Minecraft, the most important resources could be found in small deposits everywhere. I think ether the opposite or a mixture would be better.
Certain environments could be devoid of certain resources, well others have a smattering of small amounts, with some sitting on a mountain.
Going with the silver idea, think of the silver mines exploited in south america. The same idea could be used to alter the courses of civilizations naturally. A rich deposit of something causes a whole city and economic powerhouse to be built around it, by the lucky discovery of said resource and the demand. South American silver spread coinage and changed Europe.
What is the currency of Boundless?
Resource variety:
Woods- Harder woods take longer to cut and craft, but offer greater durability. Different woods offer different colors and textures.
Iron
Aluminum
Tin
Copper
Brass
Zinc
Bronze alloy
Steel alloy
Lead
Asbestos
Titanium
Tungsten
Silver
Gold
Platinum
Granite
Marble (Various colors)
Slate
Limestone
Sandstone
Flint
Jade
Chert
Obsidian
Quartz
Tourmaline
Amythyst
Sapphire
Emerald
Onyx
Ruby
Diamond