In practice, aside from the potentially "strange" appearance, there's unlikely to be a significant difference between placing an extension tube between the body and adapter or between the adapter and lens. However, there are a few potential differences:
The way light reflects and scatters inside the adapter and tube would be different. One setup might produce glare, while the other might not. Some adapters have this problem on their own. To fix it, line the inside of the tube or adapter near the sensor with gaffer tape.
Having a smaller tube near the camera (or a larger tube near the lens) may affect usability of the camera + assembly + lens.
Adapters often fit with a tiny bit of play. Usually, it doesn't affect use of the camera and lens. However, add multiple adapters and tubes, and the assembly may become intolerably loose. A smaller tube connected near the camera body would have more force exerted across it (more leverage and smaller size) than an adapter that flares out or a larger tube farther away.
One may be more convenient, or easier to use, when swapping lenses. Suppose you have an EF lens you want to use for macro, and another you want to use normally. To switch lenses with an EF tube, you could leave the tube attached to the lens, but with an EF-M tube, you'd have to take out the tube and swap lenses.
The lenses you can use with each would be different.
The prices might be different.
I have a number of adapters and extension tubes (that can attach to either side of the adapter). Most of the time, I'd prefer the tube to be attached to the lens because it's easier to swap lenses that way. But if I could have a do over, I'd skip the extension tubes.
If you're open to using manual focus lenses, consider using a helicoid adapter with a fast prime. (Old 50/1.8 lenses are quite inexpensive.) The helicoid adapter will let you use the lens normally, as well as extend it for close-up work, without having to mess around with attaching and detaching extra tubes.