[Discussion]What's really the deal with prices of variant covers?

I'm kind of new to all this, meaning I have been pretty casual for a few years and just recently started collecting current series other than Spider-Man, but I really don't get what's happening with variant covers. What I'm going to describe happens mostly with Marvel comic books but I would guess it's the same with other publishers as well.
I know that a seller can order some 'rare' (low print run) ones after they have ordered X copies of the same issue (making that variant 1:X) and that most of the variants have the same cover price as the normal ones, but the actual retail prices really confuse me.
Most have much higher selling prices from day 1, only to go even higher after a few months, and some even somehow end up on ebay weeks before release with even higher prices, practically rendering the price on the cover useless (at no point was it selling for 3.99). Even the more common variants are still a couple of Dollars above the cover price.
Is this considered normal or is my LCS being greedy? Please let me know about the price changes on variant covers and how the whole system works.