I think it also depends on riding style, terrain, and bike setup.
If you have a dropper post and a similar cleat position, than I would shoot for the same, then adjust for any differences in crank length and pedal/shoe stack height.
I used to have a hardtail and I would set the saddle height lower than my road saddle, then “hover” more often. It also gives more room to get behind the saddle when descending.
Now I run a full suspension with a dropper post, so the extra room to move when descending is less important. BUT I do use flat pedals when mountain biking, and use a more foot forward position on these pedals than on my road bike, which leads me to prefer a lower saddle height on the MTB than my road bike.
It is a pretty good starting point to measure the from the top of the saddle to the centre of the cranks, then take into account the different crank arm lengths as a starting point and then take into account the points @mcneese.chad mentioned.
From my personal experience don’t really matter how do you set it up, the main demand that it should be firmly fixed and not hang out when you riding
Also, If you can get fitted for a saddle. It will ensure you’re on the sit bones when riding.
You can then add a gel cover for more comfort. You can be sitting on a “Park Bench” saddle but if you’re not on the sit bones your ass is gonna be numb/hurt.
Hope it helps!
Sitting lower relative to the Cranks & Bottom Bracket = No*
Considering that Saddle Height is about the Saddle to Bottom Bracket relationship, MTB suspension sag is totally irrelevant in all but a few rare cases. Most common full suspension bikes have a fixed Saddle to BB relationship (notably ignoring dropper use).
If you are using a URT suspension design (where the BB actually changes position relative to the saddle), then yes, there can be a sag related issue. But as we covered in a similar comment recently, these URT bikes are all very old with nothing notable new in the recent decade. It’s essentially a non-issue unless someone is using a classic retro bike for whatever reason.
But in the vast majority of cases with any modern bike, sag has no impact on proper saddle height setup.
I have my saddle slightly lower (also on my cyclocross bike compared to my road bike). But also have my cleats as far back as they can go, so i can set the saddle even lower. On the MTB you are (almost) out of the saddle a lot anyway and having the saddle out of the way is helpfull in controlling the bike, but you have a dropper, so already know that.
But the correct answer is, your saddle height should be set correctly.
What correct is, is sort of up for debate.
I run the same pedals and saddle on my “road” bike and my mtb. So I also run the exact same distance from the bb to the top of the saddle. It works great. I don’t see any reason to run a mtb saddle lower.
I was advised by a fitter to measure from the pedal axle at its extremity which will mostly account for different crank lengths (there is off course variance which can result from different shoes/cleats). Whilst I don’t run a mtb (as much as I’d like to), measuring that way my gravel bike, with shorter cranks, saddle is circa 1cm lower than my road bike. Measuring to the centre of the BB they are about the same.
I think measuring from the pedal actually determines your actual leg extension at the maximum point regardless of crank length, which you want to be more consistent. It works for me anyway, as you say though and like I hinted to there are other factors which won’t make it easy to have things perfectly consistent (q factor, different shoes/cleats/pedals), it just removes one variance
Imo you should aim for a position on the bike where you are balanced so you don’t fall over forward when you let go of the handlebar.
Now, if you stand up straight your center of gravity is obviously located somewhere under your foot. If you bend over in a position similar to your MTB-position in order to not fall over you naturally balance your body by extending your butt reward. Now assume a apposition similar to your road bike. What happened to your butt? Even further back, right?
Saddle should be positioned fore/aft so you assume a balanced position, then adjust stem length to get a comfortable grip. TT-bikes are a different matter as the elbows can support more weight than the arms and hands.
Touched on in the other replies, MTB setup is largely about balance over the bike for control in more extreme conditions and angles (up/down) compared to road bike setup.
I tend to still aim for a leg extension that is appropriate for them and their ankling style.
Next is the fore-aft saddle position with a goal of placing them over the BB/Cranks in a way that they prefer to pedal.
Bar position is relative to the saddle after that, and aims to give a proper weight distribution via reach and height to suit the rider preference and their terrain. This is often a setup with a higher and shorter space when compared to a similar road bike setup. But some people get more or less aggressive from there.
Generally speaking a MTB setup will be short and high enough to sidestep the potential hip/back angle issues we see with more aggressive road setups. Meaning, you can likely go fairly low with the bars (and probably still above a roadie setup) and not run into hip angle impingement. That can vary if rider has injuries or other limits, so it is all something of an unknown to a degree.