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I learned about setting intonation as it's typically done for guitars. The method I've always seen in books and videos is to compare the fretted twelfth fret note to the twelfth fret harmonic and adjust the saddle position until the notes match. The builder I learned how to build guitars from did it this way too.

I ran across a video in which the intonation was set on a mandolin by comparing the fretted twelfth fret note to the open string note and adjusting saddle position accordingly. I hadn't seen it done that way before so I checked some other mandolin videos on the topic and found that the guy in the first video is not alone on this. Other videos on setting mandolin intonation use the twelfth fret harmonic method though.

My questions are:

Are the two approaches equivalent?

Is there any reason why comparing the fretted twelfth fret note to the open string note would be better than comparing it to the twelfth fret harmonic?

Is anything about this specific to the mandolin with its much shorter scale length?

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Once in a while you get shown the light in the strangest of places if you look at it right - Robert Hunter

I setup guitars with this method. I read somewhere that it was more accurate. Don't remember where I saw it. But I do know that an electronic tuner seems to be able to read the pitch of a fretted note better than a harmonic. I would think the methods are somewhat equivalent.

Edit: I think the information came from the great article on nut compensation by Stephen Delft.

https://www.mimf.com/nutcomp/

I do my setups with the fretted note too.

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Steve Smith
"Music is what feelings sound like"

Consider first that if there is any, any fretted note involved in the method we have introduced a variable and will to some degree skew results. Our finger pressure is a variable. On a strobe tuner I can pull a fretted note several cents sharp or conversely flat just with finger pressure. This is also part of the magic of the finest players in the world.... tone in their fingers.

With that said there are no methods that will yield perfect results and all methods contain one compromise or another.

I set up a 1917 Martin mando, B style BRW Ivory, etc. yesterday and have pics of it on my Facebook page. I use the same method that I use for guitars and bases comparing the 12th fretted to the 12th harmonic AND varying finger pressure several times and taking the average reading on my Peterson strobe tuner.

I typically will put all the new strings on a mando but only tension the bass and high treble strings initially. Then I set the intonation of the two outer courses of stings only moving the bridge forward or aft accordingly per the method.

This is to get the bridge in the right neighborhood. Also did you know that the points on the F holes on both mandos and arch top guitars were intended to be a starting point for bridge placement during a restring? A lot of people don't know this and it's a great help.

Then I tune the entire thing to pitch and recheck the two outer courses of strings and move the bridge however slight amount it needs to dial in the intonation.

Anyway 12th fretted/12 harmonic here and never had a single complaint about my dialed in intonation on guitars, bases, mandos and other stringed, plucked instruments.

Lastly I would not say what I do is better nor would I say the other methods are better. I can do intonation by ear pretty well too. The methods are simply different. No matter what method you adopt try to average out errors from fretted finger pressure for a higher level of accuracy.