No, red is not an indication of MDG, it's found a lot in Mdina too.
The brown colour was made using red glass, it's the silver (from the silver nitrate used) reacting with red glass that makes brown - so the streaky effect arises from unchanged and changed reds.
The only way of telling MDG by colour is if it is cased in amber, uses green glass or is the blue that is specific to MDG.
I think I've got an MDG cloudy yellow stoppered bottle too.
I reckon wonky MDG arises because Boffo was working with an apprentice on a piece during training. If you've got a perfect piece, it's probably all him or because he's got an experienced assistant at Mdina. Although I do have a couple of "perfect" bits that are definitely MDG.