Practically it's come to mean just sanitization... "don't say something nasty or embarrassing to users." But that doesn't apply here, the reasoning tokens are effectively just a debug log.
If alignment means "conducting reasoning in alignment with human values", then misalignment in the reasoning phase could potentially be obfuscated and sanitized, participating in the conclusion but hidden. Having an "unaligned" model conduct the reasoning steps is potentially dangerous, if you believe that AI alignment can give rise to danger at all.
Personally I think that in practice alignment has come to mean just sanitization and it's a fig leaf of an excuse for the real reason they are hiding the reasoning tokens: competitive advantage.