The current front opening to Espada is so narrow that during funerals a casket with pallbearers on the side cannot pass through. There are two basic theories as to why the doors ended up in the current configuration:
1) The masons simply made a mistake and got the stones mixed up during the layout phase.
2) Taking into account the smaller facade and the height limitations because of the choir loft, they made the intentional decision to make it fit the space in an aesthetically and proportional pleasing layout.
The mason who installed it could have easily used Tello's intended design by simply shortening the side pillars and moving them in a little bit. A casket with pallbearers could walk right through and the problem would be solved. But he didn't.
To get to the real reason, though, you need to know a few things about the construction of the facade of that little church.
1) The front wall is four feet thick so that it would act as a buttress for the wall of the big church. In those days they would basically build two, foot thick stone and mortar walls, and fill the middle with assorted rubble. This is why the facade wall was the only thing left standing when Father Bouchu started his crusade to bring the compound back to life around 1885.
2) Because the original wall was intended to attach to the big church, the original door was "built in" at the time of initial construction and was offset from the center. It was filled in when the other door was installed. The fill probably did not add significantly to the support of the heavy stones above it. You can see the faint outline of this door in the facade (right side panel).
3) The stones of the arch are only about 9" thick so despite the fact that the design is inherently load bearing, they were never intended to bear the weight of a large stone wall.
My final conclusion is that taking into account structural considerations like fear of the wall collapsing under it's own weight during excavation or trying to keep the rubble from falling into the opening from above, not to mention the shear amount of work involved in creating a hole almost twice as large through a four foot thick stone and rubble wall, he rearranged the stones to create an opening that just happened to have a hint of the Moorish arches. What he ultimately created was a wall that never fell, as all the others around it eventually did.
Other important conclusions:
1) The barbed quatrefoil was a popular motif in the Mexican Baroque Period (1710-1760) and it's use as an arch most likely originated in Mexico. It seems to have been brought to San Antonio by Antonio Tello in 1740.
2) The use of the quatrefoil and the barbed quatrefoil as religious symbols are traditionally of Christian origin. The example of the quatrefoil arch from Istanbul from 462 AD predates Islam by 200 years. No examples of the barbed quatrefoil have been detected in any Islamic Mosque after extensive searches.
3) Several of the prominent architectural historians that wrote about the missions during the 1960's and 1970's (Eugene George and Jacinto Quirarte) did not recognize the shape of the arch in either San Jose or Concepcion as being from the barbed quatrefoil, characterized them as a "mixtilineo arch" and attributed it as being of Moorish origin. Many books and papers written since then quote both of those author/scholars writings.
4) Evidence would suggest that the stone outline currently adjacent to the existing church at Espada is built on the foundations of the original Tello church. The larger archway that would have been constructed had the lower voussoir (arch stones) of the existing arch been reversed would have fit perfectly over the gap in that west wall.
The advent of the internet has opened up a new type of historical research: being able to search endless photographs taken by professionals, amateurs, tourists, and just about anyone with a camera. This is a powerful tool unaffected by previous statements or opinions.
Many of the previous attempts to explain the doorway acted like the stones ended at the ridge, which they clearly do not. Careful inspection shows that there was probably an outer lip on all of the stones originally and some were removed either intentionally or inadvertently.
Looking closely, the outline of the original door that was to lead from the sacristy to the church can be seem. Because it was offset it had to be filled in before the new opening could be done