1) I haven't noticed that, but I imagine that it means I did not extract that code when formatting. I will fix that if I ever make a new version. If you want to fix that, then go to around line 820 and see this:
# Codes without arguments
no_args_codes = ["\x02", "\x03", "\x04", "\x05", "\x06", "\x07", "\x09",
"\x10", "\x95", "\x94", "\x91", "\x90", "\x89"]
# Codes with integer arguments
int_args_codes = ["\x01", "\x92", "\x84", "\x82", "\x81", "\x11"]
take "\x02" out of no_args_codes and put it into int_args_codes, so it looks like this:
# Codes without arguments
no_args_codes = ["\x03", "\x04", "\x05", "\x06", "\x07", "\x09",
"\x10", "\x95", "\x94", "\x91", "\x90", "\x89"]
# Codes with integer arguments
int_args_codes = ["\x01", "\x02", "\x92", "\x84", "\x82", "\x81", "\x11"]
2) I don't understand why you would ever do that. Why call Scene_Map twice? Why call it at all? Anyway, it can probably be fixed by putting a wait command of 1 frame between the Call Script and the commands adjacent to it.
3) I assume you mean you set it in $game_ats and then it doesn't take effect immediately? $game_message.clear.
One thing to be noted is that when you do change the $game_ats, you will need to use the code $game_message.clear to make it so that they will apply to the very next message, rather than just all messages after that.
4) the skip text in the ATS does the exact same thing that the default skip does, pretty much. The default skip-on-user-input displays the entire message immediately. the ATS can't do that any faster. What I'm guessing you are seeing is the scrolling effect - it will seem fast because the skip on user input for the ATS brings the text down until the next time it needs to scroll. This means that in long messages, it will make the first line being currently displayed disappear. However, if it only brought you down to the last line than it would both nullify the point of being able to skip text messages at all since the last line at least would have to be displayed.
In the end, it's the player's choice whether to skip the text or not; if they miss information that matters than it's their own fault. If you want certain messages to be unskippable, than just disallow skipping for that message.