I think that bug is as a result of me implementing Pokemon Crystal version detection badly.
Also, in the next version I am releasing, I will be implementing some sort of #dynamic support for gold, however it will only work with 3call and 3jump commands, which will essentially void most of its usage :( Because there would be a lot of checking involved to get it to work with 2-byte commands.
For the idea about commenting each line with the size in bytes, this would not be possible for while editing the script, but it would be possible while decompiling. If you want to get the size of each "#org" statement in your scripts, you can use the "debug compile" feature of PKSVUI to compile the scripts without writing them, and the size of each script is logged in the text file.