Bob has an extended discussion with some interesting history, but put simply, your question poses a false choice. The state - any government agency - has the right to take private land for public purposes - that's "eminent domain" - but must pay for it at fair market value, undiminished by the proposed project. The value and any sale conditions (new access roads, moving things, etc.) can be established either by negotiation (resulting in either voluntary land purchase or "friendly" condemnation) or as set by a court fight (standard condemnation), possibly including a jury trial and appeals. Condemnation at a discounted (from market value) price can result in some tax benefits for the property owner, as noted by Bob wrt the Coast Line offer (failure to accept that proposal, I fully agree, was one of the dumbest moves in California transportation history).

HSR was up against it from day one, since a lot of the landowners along its proposed route obviously would not be friendly. Caltrans has a long history with such situations; it's a complex legal and procedural dance that it helps to have regular practice with. Recently saw where HSR has some former Caltrans people running the right of way process; if that's a recent change from using contractors, it should have happened way sooner.