I don't really see extra music, be it on Tape, CD or Vinyl, as merchandise... that's an extra to those who like extras and want them, that's the reason of making a limited number of special editions with extra music. Music that most probably would never been made available otherwise on that form.
Adding extra stuff to a release, such a bonus CD for example, will add a significant production cost to each copy of the special version, that's the reason for charging more and the reason for making it limited to a small amount is due to not everyone wants those extras and not everyone is whiling to pay for them. Some may overcharge it, specially when the limitation is not that limited, but that will depend on the label and the way it is managed. I think everyone knows this.
I see nothing wrong with extra music and I personally like it.
For me, merchandise is something different. Shirts, patches, pins, stickers, caps and so on, that's merchandise.
Different packaging, extra music, that's not merchandise and not useless in anyway. Extra music it's welcome, and I'm happy to buy it when I can pay for it or think is a reasonable price for what it contains.