If you have both a GoG and Steam install, it doesn't ask you which to install, which means it won't always install to the one you may be actively using.

The best way to handle that might be to show a message like this:

SMAPI found multiple copies of the game. Where do you want to install SMAPI?

[1] Install to C:\Program Files (x86)\GalaxyClient\Games\Stardew Valley.
[2] Install to C:\Program Files (x86)\Steam\steamapps\common\Stardew Valley.
[A] Install to all copies.

What do you want to do? Type 1, 2, or A, then press enter.

What do you think?

That would make the most sense.

Since usually I don't mod my Steam install, for example. I use it to test on a "vanilla" one

Done in develop for the next SMAPI release.