Well, are they being overcharged for that berth? Or are they assessed the market rent? And as for "can't pick and choose" - I disagree. I read that USSC decision and understood it completely differently from your interpretation.
Beyond that, the SCOTUS decision has NO relevance to this case. You're building assumption castles in thin air.
They're being charged a high monthly fee, while other nonprofits are not charged any fee. It's rank discrimination, based on ideology. Look up "viewpoint discrimination" in a law hornbook. The US SUpreme Court has said again and again that government can't withhold access to a public benefit based on someone's constitutionally protected viewpoint. The law school/military case wasn't about that -- the Court decided that case based on Congress's military powers under the Constitution. You need to become familiar with more Supreme Court cases - such as the Karen Findley case, the Rosenberger case, the Legal Services case, all of which say that government benefits can't be withheld simply because government doesn't like an applicant's viewpoint.
I'll ask you again: Do you think it would be constitutional for Berkeley to charge Republicans, but not Democrats, to use its Marina or its swimming pools? THat's what they're doing in the Sea Scout case - - they're charging the Sea Scouts, while not charging other nonprofits whose views are more "acceptable" to city hall.
However, the Constitution, as interpreted by the US Supreme Court, says differently: Government can't withhold access to govt programs or benefits based on somebody's viewpoint. So charging the Sea Scouts, while giving free entry to other nonprofits that are deemed politically correct -- is unconstitutional. Just as it would be illegal to charge Republicans but let Democrats and Greens in free.