If a Japanese and Taiwanese person type things with their keyboards and end up with the same bytes for different logical characters then no things do not work practically for any practical definition of "practically".
Your argument is absurd because people don't see code---they see glyphs, and using the same code for slightly different glyphs is a non-issue when they are not interchanged. (And when they are interchanged, both would see glyphs "correct" to them anyway.) Japaneses are sensitive to Han unification only because they recognize more glyph variations (Z-variants) than what Unicode originally could, and IVS is exactly a tool for ensuring exact glyphs assuming cooperative vendors. Not to mention that Han unification was already quite weakened by source separation principles in the first place.
Your argument is absurd because people don't see code---they see glyphs, and using the same code for slightly different glyphs is a non-issue when they are not interchanged. (And when they are interchanged, both would see glyphs "correct" to them anyway.) Japaneses are sensitive to Han unification only because they recognize more glyph variations (Z-variants) than what Unicode originally could, and IVS is exactly a tool for ensuring exact glyphs assuming cooperative vendors. Not to mention that Han unification was already quite weakened by source separation principles in the first place.