Why are second price auctions preferred if they don't maximize expected revenue?
I don't think sellers would prefer SPA over FPA. In fact, the SPA is riskier than the FPA, if we look at it from a seller's perspective. The reason is because the distribution of prices in case of the SPA is a mean preserving spread of the distribution of prices in FPA(you can refer to Vijay Krishna's Auction Theory for the proof). 

However, the VCG mechanism finds a lot of applications in real life scenarios(like in case of network routing algorithms). It just so happens that the VCG mechanism can turn out to be the second price auction, given that certain conditions are met. 

The Generalized SPA is another such example, that draws its basis from the standard SPA. Please see https://en.wikipedia.org/wiki/Generalized_second-price_auction .

As far as the English Auction is considered, it is equivalent to the SPA only in the case of independent bidders. If the values realized by the bidders depend upon the the values realized by others(meaning the valuations are now interdependent), the English Auction no longer remains equivalent to the SPA(interdependence is something that on can expect to be more prevalent in real life cases).

Another thing, the RET states that the 'expected revenue' is same for standard auctions with symmetric bidders. The payment received by the seller is just the highest bid. Thus, receiving a higher payment in either auction(FPA or SPA) depends on the values realized by the bidders(and the bidding strategy).