I find that by miksha batim, in the shel yad, many expert sofrim are not makpid that the whole parsha should be in the bayis, and if part protrudes into the titura they are not the slightest bit concerned. In fact, the most mehudar tefillin I check, sold with all the top hiddurim including miksha batim, often have the shel yad parsha protruding deep into the titura.
Yet by non-mikshah batim, these same experts consider it to be a chisoron in hiddur if the above occurs. They hold this (of it being a detraction in hiddur) even when the parsha does not descend deeper than the titurah elyona or the part of the titurah that is made of the same piece of hide as the bayis.
So what am I missing here? If the whole reason why we are not worried about the parsha protruding by miksha is because it's the same ohr in the titurah as the bayis, why be concerned in regular batim when the parsha does not protrude lower than the "filler" and still stays in the space of the upper ohr which is the same ohr as the bayis as well?
If someone could fill me in, I would like to understand this discrepancy.