PDF is created by Adobe pdf library, I guess, and also rendering pdf to screen representation. If it is true, Onyx cannot do much about it.
But I found sort of the solution. Not perfect, but better than nothing.
If Onyx knows that there is this one or two bugs in Adobe they could go around in following way. Check if line is perfectly horizontal or vertical and if so make it not exactly
vertical or horizontal by moving one of the ends 1 pixel. (Or they could cut the line to two sublines and missaalign the middlepoint, so that endpoints would be unmodified.)
It should not make any harm for long lines and be quite OK for short ones. It is better to have slightly modified line than no line.