I mean, there are basically two standards. One's to just have them seen from directly above (while being impassable) as you see in DF &c. so that you can clearly distinguish everything; the other is the ToME style, having them be side-on like that but also making the sprites block movement on their tiles with maybe a tiny bit of overlap. In the case of the latter, pretty much everything is slanted at the same angle, though, which doesn't really mesh well with the top-down view that games like this tend to require if they're not going to be utter headaches to eyeball distances in.
There are some games like Elona+ where trees do work like you have them, but those are generally tick-based and cede direct control of the character to the player so there's not really that same degree of "goddamn it where's my guy" when you can just tap right or left a couple times. More importantly, pretty much every game that has that (at least for me) ends up with the sole memorable type of tree-related interaction or thought being "oh hell, which tree am I behind?" rather than anything positive.
I mean, it can work, but I'd suggest something like finding/making/altering tree sprites so that they're a bit more limited in their coverage of background tiles. I can say right now that if I were to play that I'd just start straight off by deforesting the map, both so that I didn't have to hunt down my dudes and to make an open kill-zone that enemies couldn't wander through half-invisibly. They don't have to be to scale to convey what they need to, as Rimworld showed--those trees are, what a tile of trunk and a tile and a half of concealing foliage?