About...3 seconds to work out that a tree is a tree and not something which doesn't exist. Less if they follow the tutorial and understand that the "look" command and z-levels exists. If there were stumps and constant confusion over which is which you'd have a point.
As I've said before, I'm a big Vanilla person myself, but the Steam/etc launch is supposed to be visually intuitive (and also we don't know if the Look command will raise or lower in prominence in the UI bit of the revamp - though I would hope it would not be subsumed somewhat, games with nice graphics tend to only need cursor-looking for details of tiles, not a full explanation, so...) and in other top-down all-way-scrolly adventures or area management games they tend to leave "stumps" when trees are felled (by efforts of player or pre-supplied 3rd-parties) that may or may not fade away/fail to refresh after leaving the locale but generally don't just have trees vanish without remains. (One or more versions of the Settlers franchise, IIRC, felled a tree sideways and then would leave the outline of removed side-branches as the Log resource was hauled off by the woodcutter minion.)
The only other game I can recall such behaviour is Minecraft, and (without a mod, at least in the old Beta version I last played it) that has antigrav wood that means you can slice off its bottom and/or middle trunk and you still have higher trunk visible (and leaves only vanish when deprived of their progenitor trunks or trunk-sized branches) and even then what
looks like a cut-off stump is in so me meaningful way an actual cut-off stump. Even if the tree crown is also still hovering a few Zs above it.
Yes, it's a trivial point that the stump section (and roots, not normally an issue in more surface-bound games) just vanish, and so stump-parts are still connected to at least
some more tree at higher Zs, but let us not more realistically depict things that aren't actually what the thing technically is.
And though the radially(-inward) shaded version of the "stump" is slightly less stumplike, I'm not sure whether it yet looks unstumplike enough for my liking (on behalf of those newcomers I'm pleading o behalf of). Not sure what I'd do, though.
TL;DR;... it
may be no more than a moment's confusion, hopefully, but I think it should be mitigated further, and ideally avoided. Good luck with that!