I still don't really get this one:

https://www.deviantart.com/cyangmou/art/Pixel-Gameart-101-687177800

What I figured out so far is that the height of my circles are half of the width. But let's say I have to make a tree how do I know how big the top part is and how big the front is?

Because let's say the tree stump in the tutorial is taller and the hole stays the same size then the ratio is lost, right? So on what ratio do you base the sizes on? So how would you edit the ratio for it to make sense with a taller trunk (front), but same hole size (top down)?

Also according to my circle ratio I should make grass that is more top-down than frontal, but frontal grass just looks so much better...

You should be working with cubes, basically. Which is what Cyangmou put there to illustrate and to give a reference.

Being isometric, every width is the same, every height is the same... He did use some perspective there, though (1-point persp), which doesn't make much sense to me, because your other assets would seem inconsistent when you placed them side by side. They would each point to a different, erhm, point in the horizon.

If you're not working with tiled assets, though, and are just making a "scene", then you would make every asset follow the established perspective, its VP(s), horizon line, viewer angle, etc.

Actually, fuggedabout that. Draw a grid and pull lines up from it. If you need to find the center of a "square" draw an "X" connecting its vertices diagonally.

A circle should touch the middle point of each edge of a square, and if it's in perspective, then use the "X" trick to find those middle points.

I'm pretty sure drawabox will show you how to do this, so you should check that.

The size of a square on a grid is unimportant if you're not working with tiled assets. But if you say it's "1 meter" in length, then you all of your assets would be based on that measurement.

You may want to stylize, though, and make assets that are, say, chunkier, more chibi-like, so proportions wouldn't work the same as in real life. But you would still have "your meter" to work with.

As for the grass looking better in frontal, than in top-down perspective... Well, that's for you to decide. If you use frontal view it will look inconsistent with the rest of the assets, but not necessarily bad.

Does that answer that question?

Just in case it doesn't here goes a TL;DR:

Make a grid using the perspective you want. Practice drawing simple forms in it. Cubes, Spheres, Cylinders, Cones. Then base your assets on those forms.