As a consumer and fan of homebrew releases, I can understand your point on this. A lot of people buy the game simply to play the game and the rest is clutter. But at the same time, the collector in me disagrees because as a collector, I make a purchase CIB so that the homebrew purchase will mesh in well with the actual releases, as well as to increase the overall resale purchase of the collection, should I ever decide to sell it.
If anything ever deterred me from collecting CIB, it is the fact that with boxes and all, collections for multiple systems will clutter up valuable space. But that is the price to pay when one is a collector.
I like the idea of homebrewers offering the option of whether or not the purchaser/collector would like to purchase their game CIB or not, and I would support it and applaud it should it ever becomes an option. But ultimately, that will only drive up the prices of the games as a lot of printing companies give a discounted prices on their labor when ordering in bulk. So as long as collectors who demand CIB exist, then the homebrewer has to do what will save them cost-wise on production.
As far as instructions go, with the exception of Intellivision games [which provide controller overlays to assist in game play understanding], many gamers need to understand what the homebrewer is intending for us to fully enjoy the same. A lot of games today, because they offer plenty of space, offer tutorials built into the game, which is awesome. But I somehow doubt that this could be done on many retro systems, although INTV Corp. games did dedicate on-screen controller descriptions to avoid the cost of producing controller overlays, and thus saved some production costs.
If I had one gripe, it is that I was never fond of shelling out $70-$100 for a homebrew game [especially for systems like Atari 2600 and Intellivision], when I can buy a brand new game for Xbox One for $60. But again, it comes down to the purchaser having a deep love and kindred connection with their retro system that justifies it.