A compensated saddle is just one setp to achieving correct intonation.
You mentioned that you tune your B string slightly flat.
A compensated saddle does the same thing.
There are several components that all have to be adjusted to each other to get the best intonation.
The cheapest and easiest, is the saddle.
If you tune your guitar harmonically, you will find where the intonation is out.
Now by compensating the saddle either forward, toward the nut, or backword, you can slightly adjust the distance that the string is from the nut to the saddle.
By doing this, you change the pitch slightly sharp or flat.
This is more difficult to do on a 12 string but is even more important in my opinion.
Because the 2 Bass E strings are such a differern size from each other, when they are both in tune on open position, they will go out of tune when you fret the guitar and play, say a G chord.
The larger string will go sharp.
Compensating these 2 strings so that they are more ballanced, will help to make the guitar stay closer to being in tune as you play up the neck, or use a capo.
I also see many cheaper guitars that have compensated saddles from the factory.
These saddles are plastic and they are formed compensated.
Just because they are compensated, doesn't mean that they are correctly compensated though.
A Guitar Tech will make a compensated saddle that is adjusted for your guitar, as every guitar is slightly different form each other.
I have compensated bone saddles in most of my guitars.
One or two are close enough with the factory saddle, or a bone saddle that I have made so they don't have fully compensated saddles in them.
I do compensate the B string on the saddles that I make.
I don't have the tallant to make fully compensated saddles.
