Mishnat Sofrim brings from Beis Yosef that the nekuda tachtona of the Aleph should be 1.5 kulmusim from the top of the body.
Traditionally I have always read explanations that describe this parameter as being the distance of the leg of the lower yud, as shown in the picture below (this is an aleph I've written previously, not for the purpose of this post so isn't geometrically accurate for this purpose).
My STa"M rav and teacher suggested that this poses two potential issues. In order to comply with this, since the width of the gag and the yud are both 1 kulmus then it would mean that the total height of the Aleph would be 3.5 kulmusim, which seemingly is not in line with the principle that the 'square' letters (eg beis, dalet, etc) should all be 3 x 3, here the Aleph would have to be bigger than the others. If you want to say that the Aleph is 3x3 but the lower yud protrudes lower that the guf by 0.5 kulmus, this then contradicts the gemara that the words of 'emes' stand on 2 legs.
My rav therefore suggests that the 1.5 kulmusim could be measured from the top of the gag to the beginning of the regel, shown below (again not to scale). This would a) solve the 3x3 issue and b) aligns more with the wording of the beis yosef that it should be distanced from the gag 1.5 kulmusim.
I would love to hear comments!