Give that alleles are different codings of the same gene - does that
mean the different alleles are the same length? It must also be true -
right? - that different alleles encode for different proteins (else
there would be no difference in their manifestation.)

Assuming two samples of DNA could've - but not necessarily - come from
different species, if at a particular locus the DNA is different, how
does one know if the difference distinguishs different alleles or
different genes? .

Thanks.