When there is a penalty, the pop up just says something like (I don't have it in front of me) "Play result was 5 yards" but sometimes it is actually a loss of 5 yards.

Or to use a math term, it is showing the absolute value of the resulting yardage. Can you edit to clarify if it is a gain or a loss?

Also, it seems that if a "before snap" penalty happens when it's less than 5 yards to go for 1st down, the LOS just moves forward but does not grant an automatic first down.

So I could have a 3rd and 1, then the D has a neutral zone infraction, and then it's just 3rd and --, and literally the LOS is ahead of the first down line.

Does that make sense?