Yes, Thompson "would be perfectly content with it [1st & 2nd amendment] being thrown out." But Collins plaintiffs only challenge the 3rd amendment. Because they have realistic ideas about what is legally enforceable and what is not.
Therefore Thompson kind of lied: "....we are perfectly content with all of these arrangements [HERA], which, as we say in the complaint, were a concrete life-preserver." That's what judges and the government like to hear.