Times, they are a changing...
The RV-14 uses hardware that is not familiar to a lot of people (teaching tech. counselors and certification inspectors will probably be part of the RV-14 building process.
Take a close look at the MS nuts that are being used. They are not nearly as tall as the AN365 nuts we are all so familiar with. Because of this, the standard rule of thumb for # of threads showing will not work.
In fact if used with these nut, it could cause a bad situation.
Example - There are many instances where if a shorter bolt is substituted, one of the parts being bolted will be baring on the threads of the bolt instead of the shank. Not a good thing.
In instances where the bolt is fastening a part made from thin material (lets say the flange of a rib) it is important that the shank of the bolt protrudes fully through the rib (so that the thin rib flange is not baring on the threads of the bolt. If you installed a shorter than spec'ed bolt to attain the standard 1-3 threads visible, because you are using an MS nut, the rib flange would have to be baring on the threads to have the proper # of threads.
It is good practice to double check the specified hardware, just make sure you are using the proper standard when making that judgement.
Repeat builders, building an RV-14 will likely notice the use of a lot more thin and thick washer combinations. The reason is for specifically dealing with proper bolt lengths with the use of MS nuts.
I recommend that builders make their cross check judgement based on the length of the bolt with all washers in place. Then decide if it looks like there is any danger of the nut bottoming out on the threads (often referred to as shanking out). Keep in mind that in some instances, torquing the fastener will pull everything more tightly together, possibly still allowing the nut to shank out when fully torqued.
BTW, there may be some instances where the fastener shank does not protrude outside of a thick part. Because of the additional part thickness, it is not possible for it to bare on the threads, so a slightly shorter bolt is used.
2nd BTW, the 1-3 threads showing standard has never applied to fasteners installed in nutplates. Take a look at the threaded portion of a K-1000 nut plate. There is a large amount of relief in the threaded area that will allow a fasteners shank to penetrate before shanking out.