The question takes one sentence in the Nature Scitable article about alleles out of context. The statement:
“Humans are called diploid organisms because they have two alleles one
from each parent.”
is not the actual definition of allele in the article, which is in the first sentence:
“An allele is a variant form of a gene.”
Rather, it is part of an explanation of the situation for variants in humans. (It is not meant to be a definition of diploid, either.)
This is perhaps clearer in the definition for allele given in the respected undergraduate text, Alberts’ Molecular Biology of the Cell, where the same two ideas follow one another directly.
One of a set of alternative forms of a gene. In a diploid cell each
gene will have two alleles, each occupying the same position (locus)
on homologous chromosomes.
The first sentence is the definition, the second sentence provides an example of the variants in diploid cells.
As the Wikipedia entry explains, the word allele is derived…
…from the Greek prefix ἀλληλο-, allelo-, meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, allos (cognate with Latin alius), meaning "other".
Thus it encompasses the idea of variation or difference (rather than gene homology) which is what it was coined to describe.
It is possible to refer to alleles that are identical, but only in a context where variation is possible. Consider the four possibilities for the mutation, m, of a wild type gene, wt.
1. wt wt
2. m wt
3. wt m
4. m m
We can refer to 2 and 3 as having one mutant and one wild-type allele, and 4 as having two mutant alleles (or both alleles mutant). But what about 1? It is natural to refer to this as saying both alleles are wild type, and indeed almost impossible to avoid referring to them as alleles. They are both normal, and therefore not strictly variants, but they are alternatives to the mutation at this same position.