There are at least two penguin colonies accessible in Punta Arenas. One, of which, is a bus ride and is shorter than the Magdelena Island tour. I believe it was only a half-day tour, as I recall. Obviously, we didn't take the shorter of the two. I don't think all of the cruise lines go to M.I.
In Puerto Montt, we hired a private guide, just outside the port. He took us for a lovely tour of the lake district, volcanoes, falls, the condor, Laguna Verde, etc. It lasted from about 8:30 A.M. and we returned about 1:00 P.M. The cost was about $70 plus we gave him a tip because he had done a fine job. Then we walked around town and went shopping.
Yes it was Buenos Aires to Valparaiso.