@cdiener and @Midnighter sounds very good to me. I like the warnings a lot which notify the user that something strange is going on in the mode. I agree the reversibility and flux bounds should be secondary, but definitely in agreement with the SBO.
@cossio currently not. However, it should be pretty easy to implement it in its own package. The actual linear problems don't look too complicated. The major idea is that cobrapy implements only the most common algorithms and everything else usually is its own package building on top of cobrapy. For instance like all the one at http://opencobra.github.io/cobrapy/packages/ .