Oh! I can fix the letters thing you mentioned, oops. I'll try to remind myself to do that when I have some more time, which may be a bit.
As for the indicators thing... huh, honestly, I hadn't thought of doing that. I'll try to take a note on that to add that soon. There's definitely changes to the level layouts, but they tend to be things like fewer or more enemies so it can be pretty subtle sometimes. At its core it was added to make routing for scoring more complicated overall, but uh... yeah I probably should indicate when you've gotten a stage change better in some way.
Also, yes, the optional objectives don't change the ending, and don't have anything to do with the radio transmissions. (The radio transmissions are... a really, really easy to miss visual easter egg, I'll say that much, given nobody seems to have found them after all this time.)