As someone who worked on the fan patch (back in the day), I'm not too upset that they have a lot of these formatting errata. What bothers me is that I know exactly how to fix them, and how easy it is to do so.
The issue is that the text is just in a plain old document. Probably a .csv or similar (that's how we organized it). It is often difficult/impossible to know how it will look in game until you actually put the text in the game. That said, most of the issues require a very simple fix.
Take the prefix boss issue, for example. The localization team would just see a field and they would input the appropriate English. The issue is that these prefixes were all kanji in the JP version, and there's no reason to provide a space when using Japanese font systems. The fix, however, is extremely easy. Instead of the text field reading "Vain Husk" it should be "Vain Husk " or even "Vain Husk: " if you want a colon in there. the same applies to the spacing of planet/area names, etc.