The pledge level with free expansions for life was a VERY VERY good deal.
That said, if there are boxed versions of the expansions available, I'll definitely be buying those even though I do qualify for free expansions.
To be honest I find it hard to gauge what the younger fans / those that did not play Elite from the start want these days. Some say they want it all electronic which is fine. Some, like me say they would rather have physical items AND digital (people like me). That being said, and that 90%+ of what I get is all physical bar things like Humble Bundle, GOG etc I would not always go for a "collector" edition. In fact I only have a few that fit that category, most are just the normal standard release. Digital is convenient sure but I would NEVER go for digital only if there is a physical version as well I prefer physical items. I see all kinds of Collector's editions for games out there for modern titles but they are definitely specialist items...or at least they are here in Australia. Most it seems are fine with digital downloads.
I guess it is akin to "I have the physical magazine" vs "I have the digital copy". One would argue the physical one is more "valuable" to collectors eventually etc and there is no "thrill of the chase" trying to get a digital one vs a physical one. It is all a matter of perspective I guess.
That is something I sadly miss from games these days. Not that there is much for me to buy these days, I mainly get humble bundle titles and GOG. Sure I can buy separate strategy guides but I miss BIG manuals, maps and other things in there. Look at the kind of great things Infocom used to put in the package, it was an experience in itself. Whilst I know some will just go for the digital copy I look forward to the time I open up that premium box. I'll probably film myself doing it too and take a stack of photos.
At the end of the day it is all about choices and markets. You cater for digital only, you cater for physical and a combination of both and you cater for premium collector's editions etc and everyone is happy. I guess the most important thing is we enjoy the game and if the extras mean something to you, you can get them.