Why these patterns show up so often
Most of these issues trace back to how e-commerce platforms are set up by default. Templates generate product and category pages automatically, which is efficient for launching a store quickly but leaves structural decisions unmade. Nobody chose the category tree deliberately. Nobody decided how variant URLs should be handled. Those choices simply happened as a side effect of adding products over time.
Addressing them does not usually require a technical rebuild. It requires reviewing the existing structure with a specific lens, then making a set of deliberate changes to titles, category groupings, and internal links. That review process is what the program's first three modules are built around.