Indel normalization involves left alignment and removal of extra bases; see e.g. http://genome.sph.umich.edu/wiki/Variant_Normalization .
As for the variants being biologically identical, sort of, but you can't merge them into a single biallelic variant, so it's critical to keep track of ref vs. alt to avoid accidental merging. In the blog post example, the pre-normalization reference allele was AG and the alternate alleles were A and AGG, and each post-normalization variant represents a single deleted/inserted G. So, if a sample has the A allele for both variants, it's missing *two* G bases relative to a sample with the AG allele for both variants, while a sample with one A and one AG is in between.
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