Does the most common definition of "allele" include a change in phenotype?
Yes, allele is an alternative form of the same gene which can be produced through any variations/mutations of a gene, such as deletion, segmental duplications, inversions, insertions through transposons, even a SNP or point mutation (http://en.wikipedia.org/wiki/Allele) and as correctly stated many alleles do not produce any observable/discernable phenotypic variation. A gene can have many alleles in a given population, but do not confuse allele with gene homologues (which I suspect what you were alluding to above in the second paragraph), which are similar versions of a gene such as RIN1, RIN2 and RIN3 (http://homepage.usask.ca/~ctl271/857/def_homolog.shtml).