I do recall someone saying that Alden cuts the heel area leather (the heel counter area I think it's called) slightly differently for BB tassel loafers at BB's request, but that the difference is . . . hardly worth mentioning.
There is a difference in the BB version of the tassel loafer:
In the years that followed, the tassel loafer was introduced to upscale traditional clothing stores around the country. Then, in 1957, Brooks Brothers, at the height of its fame as the Ivy League emporium, approached Alden and expressed an interest to include the shoe in its collection. "Especially for them," Clark explains, "Alden produced a tassel loafer with a distinctive decorative foxing at the back part of the shoe, which remains exclusive to Brooks Brothers." The foxing is the raised stitching on either side of the heel cup. Regular Aldens have a plain heel cup with a strip of leather up the back seam.
Quoted from: http://www.cigaraficionado.com/Cigar....00.html
Apart from the tassel loafer, I believe all BB versions are identical to Alden. Although there might be times when BB carries a certain style that Alden has at that time not in their main collection. (I remember seeing galoshes oxfords at BB but not at Alden). Yes, Alden repairs the shoes they have produced, regardless of the name they carry.