This question was taken up by the author Zvi Zohar on his book Rabbinic Creativity in the Modern Middle East. I will give a summary of what his sources tell us, and then give useful quotes from the book itself.
Synagogue orientation/construction is based on custom, not halakha. As with any customs that develop their origins are often muddled and sometimes blasphemous. In general the design of Ashkenazi synagogues are either based on the church designs of their Christian neighbors, or as a response to their Christian neighbors. The same can be said of Sephardim with their Muslim neighbors.
So while it is true that the Rambam in his Mishneh Torah describes the ideal location for the Bimah being in the Middle of the Synagogue, Yosef Karo (Kesef Mishneh ad loc) comments on this Rambam as follows: "its positioning in the middle is not obligatory, rather it is contingent on the place and time."
So you have large sources on both sides of these arguments. So now let's take a look at some of the sources brought down by Zvi Zohar in Rabbinic Creativity in the Modern Middle East pages 291-292:
In nineteenth century Europe it became common practice in the Reform movement to position the bima at the front of the synagogue hall. In reaction, the Orthodox rabbis, led by the Hatam Sofer (Responsa Hatam Sofer, Orah Hayyim, Responsum 28), ruled that there is an unequivocal obligation to situate the bima only in its traditional place --i.e. in the middle of the synagogue. This reaction reached its height in 1886, when 100 rabbis signed a declaration excommunicating anyone who prayed in a synagogue in which the bima was not located in the center.
It seems clear from the sources that the Reform movement seems to have permeated into common Ashkenazic practice despite the Orthodox movement's best efforts. Contrast that to the reponse of the former Chief Rabbi of Egypt Rabbi Aharon Raphael ben Shim'on (in his responsa umiTzur Devash 3b) in 1896.
If situating the bima in that place (the center) would impair the beauty of the synagogue, or, if in that location the bima will lack clear light, such that the Torah reader will not be able to read comfortably and will not be able to peruse the letters of the Torah scroll and to verify that the spacing [between the letters of the scroll] is at it should be, then that which is lost is greater than that which is gained....Thus it seems, in my humble opinion, ...that the bima should be set in the place most conducive to the fulfillment of its functions.
Zvi Zohar brings ample evidence that Rabbi ben Shim'on knew of the Hatam Sofer's ruling but clearly did not agree with it. Rabbi ben Shim'on's ruling is consonant with the position taken on this issue by one of the greatest Italian rabbis of modern times. Rabbi Yishma'el haCohen (1723-1811) in his book Zera' Emet details his response to a similar question. A synagogue was destroyed in which the "duchan" was in the center of the building and now the synagogue was being rebuilt, and the members of the community wanted to put the "duchan" somewhere else. Rabbi Yishma'el haCohen ruled in accordance with Karo that there was no obligation and that such a decision "everything is in accordance with the time and place...and there's nothing more to discuss on the matter."
It is worth noting that Rabbi Ya'akov Shaul Elyashar (1817-1906) who was serving as Rishon le-Tzion at the time ruled against both Rabbi ben-Shimon and Rabbi Yishmael haCohen to side with the Chatam Sofer which was not surprising considering there was a larger amount of Ashkenazi influence in Eretz Yisrael than there was in Egypt.