Ed -- if you need more info, Stewmac's "Free Info" offers a scale length calculator that includes compensation, etc.
To answer you question about do you need to worry about this -- yes, absolutely.
The 25.4" scale length, for example, is the "nominal" scale length, and the actual scale length is 25.34" in some cases (but not all). If you were to set up your bridge so the center of the saddle slot between the D and G strings was exactly 25.4" from the edge of your nut, your guitar would be in tune only in the open position. It would not play in tune at all.
Also, the type of string you use will require a different amount of compensation. Compensation is an allowance for the stretching of the string when it is fretted; when it is stretched, it naturally sounds sharper than in the open position. The lighter the string, the more it stretches and the more compensation required. So, with your 000-28, depending on how you've braced it, you might have the choice of using medium strings instead of light strings if you want. If you go for the medium, the required compensation will be less because the metal is thicker and stretches less
Varying string thickness is why different compensations are published for the same scale length -- but the people who put them out there for us leave out the important part: Which gauges of strings these compensations apply to. More compensation than the perfect amount will give you strings that fret slightly flat, and the human ear does not hear flatness of pitch as easily as sharpness of pitch; that is, sharpness is more "irritating" to our ears (as in the sharp B string in a 1st position D chord, when the B string is perfectly tuned open). Also, since the guitar is an instrument that cannot -- can not -- be perfectly tuned, it is all an approximation. (Mike Doolin's website has a great primer on intonation explaining this. http://www.doolinguitars.com/intonation/intonation1.html
. At Healdsburg last year, he told me the main figure to remember is 15/1000's inch, which equals 1 cent on a 25.5" scale with a medium unwound string. Thats how exacting it can get. I can't begin to measure 15/1000's on the break point of a saddle!)
I wish string makers would publish their recommended compensation figures.
Basically, though, if you're using lighter strings, tend toward the greater amount of compensation. Measure the nut to 12th fret distance, then repeat that distance plus compensation from the 12 fret to the saddle. (And, the amount will vary depending on whether you are measuring to the center of the saddle between D and G strings, or measuring to the center of the saddle at the high E string. )
John, above, is measuring to the High E position, at the edge of the saddle slot. That's also how Martin does it, too. I have always personally thought that the intonation on Martin guitars pretty much stinks, and I'm not alone in that opinion.
Stewmac's instructions tell us to measure to the center of the slot between the D and G strings. Different strokes for different folks -- the trick is in discovering which point of measurement is being offered as "correct" before you do your own measuring, and which gauge of string set it is talking about.
Do lots of reading. The AG Mag Luthiers Corner has some good threads on this: search for intonation, scale length, etc.