If you don't feel right about buying the Rune ...
don't buy it. Seriously, walk away, you won't be happy....BUT...
As an owner, who like SiteData, had a deposit on the Rune a year before it came out, had no problem paying the price after seeing and riding it (I didn't pay a premium), and loves the bike for what it is, understands what it is not, realizes full well the uncertainty of anything as speculative as "limited production" moniker from a huge worldwide manufacturer, I could care less what anyone else will pay for the bike right now. I'm happy and I'm not selling it, so the current market value is a moot point, unless I buy a second one.
As someone who is contemplating buying a Rune now, consider yourself fortunate you can buy one at a reduced price!
It boils down to this, (really regardless of what the item purchased)...the happiest owners are those who bought the Rune because it stirs them emotionally, before AND continuing after the purchase...not those who looked primarily at "what its worth".
None of the pricing "issues" takes away from the fact The Rune is an amazing bike, especially considering that it IS a production bike. There are many so-called custom Harley clones that (basically look alike) cost much more than the Rune, and are not near the level of fit, finish and dependability, or look as custom, lol.
I can understand The Rune is not for everyone, for a number of reasons, and frankly that is one of the main reasons I purchased it. It will ALWAYS be a niche, NEVER be a mainstream, or commonly seen bike. Period, regardless of price.
Ironically, before I bought the Rune, I figured it'd be primarily a seldom-ridden toy...it turns out to be the bike out of seven (all are very cool in their own ways) I choose most frequently, pretty much my daily rider and that as they say..."SAYS IT ALL."