Legally speaking, you're entirely correct but that doesn't escape the very point of the referendum which was a vote on that the UK as a whole wanted. Politically speaking, ignoring it would have been dangerous in the long run. Ultimately your objection has no force anyway because Parliament acted and Parliament is the expression of democracy in the UK.
In 1979 51% of people living in Scotland voted for their own parliament but they were denied it because the empowering Act required 40% of all those eligible to vote to vote in favour. That rankled for two decades in Scotland. Were the Scots just moaning?
I expect in the next decade there will be a border poll in Northern Ireland. If its residents vote by 50.0000001 to unite with the Republic will you say that's illegitimate?
I expect there will be another indyref in Scotland. What about that? Should there be a supermajority?
Back to LRM: I think it's a sad day when party apparatchiks can have such influence. His career as an MP is ended, at least for a parliamentary term and even he does not know what's alleged against him.