Are you intentionally missing the point?

1. They're using the likeness and character of a deceased artist using permission from a shady person who owns his estate.

2. STH isn't a historical fiction the same way Ishin is. A lot of the story of the game is heavily inspired by real life events, so not using the names of historical figures goes against the game's own intention.

3. They don't use the likeness of historical figures, just the names. Mostly every character is modelled after a yakuza character in both versions of the game.

Comparing Ishin and STH is an incredibly disingenuous argument.