Scale tuning (temperament) can be fun to fiddle with just for experimenting, but you probably won't actually use it unless you're playing along with a small ensemble that is using a different scale tuning
and if the song allows for it. An example might be a string quartet.
The basic idea is that when using equal temperament, your intervals (and thus chords) sound decent, but the harmonics are not perfectly aligned. The math just doesn't work out ideally, but it comes really close.
So any scale tuning is a compromise somewhere (or, a little bit everywhere...).
And, yes, whenever you change the tuning of an instrument's scale degree to make the harmonics exact for a particular interval, you usually make another interval sound worse. Really bad ones end up being called "wolf intervals". Yeah they howl. A string quartet or vocal ensemble can adjust the tuning of a scale degree on-the-fly to prevent this, but a keyboard cannot do so as easily, so in some cases you may find yourself just sticking to equal temperament even then.
- Greg