Correct. It wasn't the Court's purpose to decide the legality of secession, as that was not the issue at hand, and the majority did not entertain any argument that it should not be legal. It just proceeded from the a priori assumption that the wartime government of Texas was illegal while deciding the disposition of the bonds in question. Chase, himself, just made blunt and unsupported claims about Texas' "indissoluble" membership.
Chiles (appearing with White) argued that the then-current State of Texas was trying to forward a legal paradox by claiming itself, for the purpose of nullifying the sale of bonds, to have been invalidated whilst at the same time also claiming to be a valid complainant party for the purpose of establishing standing.
In order to preserve his desired outcome, Chase had to concoct that argument that the legal term "state" was a vagary which could refer to any combination of three things: the territory in which a legal state resides, the people who compose a the political body of a legal state, or the legal institution of a state's government. Chase separated these three things and addressed only the subject of the legality of the seceded government.
By claiming that the seceding government had exited all legal reality while leaving all corporeal and terrestrial matter behind (in a weird, twisted, backwards rapture), Chase presented a sort of "Goldilocks" zone within which the US could have legally conducted otherwise unconstitutional measures within its constitutional domain, or constitutional measures beyond its constitutional domain, or, basically, just whatever.
Chiles had argued that it was an either/or legal dilemma; that either Texas had been in (and the bond sale was legit), or that Texas had been out and then conquered (and therefore not recognizable). Chase found a third way that doesn't really precisely address popular secession or the removal of territories by arguing that, it this particular case, the people and the land of Texas just happened to still be within the United States because the seceding government had delegitimized itself, voiding the ordinance of secession. This allowed him to rule against the party actually claiming that secession was illegal while preserving an outcome which depended upon it being so.
The Supreme Court did not FIND secession to be illegal, it derived a conclusion from the prior assumption that it just WAS.