There's a lot of good information on the web, and a lot of bad information. It's gaining enough basic information and understanding on a subject to be able to sort out the wheat from the chaff that's the biggest hurdle to using it.

The scale length is defined as twice the distance from the nut to the 12th fret. This is easy to define and works for all fretted guitars and basses.

Because there is a very small area at the end of each vibrating section of string that forms the transition between the string being held firmly and it being free to vibrate, (about 1/2 a string diameter at each end) the true vibrating length of the string is a little bit shorter than the distance between the nut and the saddles.

As you fret a string, you press down on it and increase its tension. Increase the tension and the string produces a higher note.

Combine those two factors, and you'll find that the intonation distance between the nut and the saddles will always be a bit longer than the nominal scale length. So if you position the bridge so the saddles are at the nominal scale length, they will always have to be adjusted backwards from that position in order for them to be intonated so the 12th fret note is an octave above the open string note.

In general, the thicker the string, the longer the intonation distance will be. So on a 4 string bass, the G saddle will be set furthest forward, then the D, then the A with the bottom E furthest back (and on a 5-string the low B saddle even further back). For guitars, with a mixture of plain and wound strings, the wound strings take a bit less pressure to fret than an equivalent diameter plain string, with less of a tension rise, so you'll often see a wound G saddle slightly further forwards than a plain B.

And the higher the action (and I know some bass players like a good high action so they can really dig in when playing), the longer the intonation length due to the increase in tension when fretting. I've just measured the difference in intonation position on my Peavey Cirrus bass, and the E is 10mm further back than the G string (which itself is about 1mm back from the scale length). But I've also set up basses for others where this difference is nearer 15mm.

So, given that the saddles will always have to come back from the nominal scale length position, there is no point not having the saddles set forwards, with just a couple of threads showing at the front. If you position the saddles so the scale length is set at the middle of the saddle travel, it is very easy (depending on the bridge design and the length of intonation screw adjustment available) not to be able to move a saddle back far enough to correctly intonate the string.

On bridges with springs on the intonation screws to keep the saddle pushed forward, the spring can often end up be fully compressed preventing further movement. You can cut the spring down to gain some more movement, but its not ideal. And then with both string-through and top-loading bridges, the string itself will stop the saddle being moved right back, so there's less room to play with than might initially be apparent.

On the standard Fender P- and J-style bridges (and on barrel-style tele bridges), the further back the saddle goes, the more the front end of the intonation screw is forced up into the air. Too far back and the end of the screw can stick up above the strings, which is less than ideal. Again, this can be fixed, in this case by cutting down the screw length, but again it's not ideal and shows the bridge isn't positioned as intended.

Which is why setting the saddles most of the way forwards when measuring the scale length is the best way to have them for positioning a bridge (in my opinion anyway). No drawbacks, only benefits.