"I don't think the boss analogy stacks up. I compare it more to our funding of the NHS- we 'pay' a doctor's salary but can't comment about the holiday that he chooses to spend the money on as it is a private matter, but we can comment on the new furniture he orders for his surgery because that is NHS business."
If the Doctor chooses to spend his own salary on getting a very decadent chair for his office that's been made from the nose hairs of a million hand reared Scottish gerbils then that's the Doctor's own concern. If it doesn't come out of money that he's given to run his surgery then it's not our concern and we can't claim that we paid for it.
Likewise the Civil List is the "pay" for the Queen. She does actually get an allowance for her "state" related work.
"The wedding was a state occasion and so the Royals are accountable for the spending of the money."
No it wasn't a "state occasion", had it have been then maybe the tax payer would have picked up the bill as it did for the Wedding of Charles and Diana.
"The crown lands belong to the crown rather than to the Royal family personally."
Yes, but they used to belong explicitly to the Monarch and the Monarch received the income from them. That income was given up in exchange for the income from the Civil List in a deal that is apparently renewed by every new Monarch (which raises a question, could they say "stuff this, I'm keeping the income from the estates it's many many times higher!"?).
So their status is somewhat special, which is good, because as said it's probably stopped David Cameron from trying to flog them to his mates in the same way that he tried to sell our forests.
"It's not 'making stuff up' but a difference in perspective."
Claiming that because we pay them £x in exchange for them giving us about 20 times that amount we can say that we paid for the Wedding is a very strange perspective indeed.
That is basically a business deal, and despite a similar deal my bosses would not be welcome to come to my house and claim that they paid for my TV.
And the launching point for all of this was your statement that "It's paid for by the taxpayer, unlike everyone else's wedding, and people should have the right to object to that if they choose."
It wasn't paid for by the tax payer.
Regardless of not paying for it the public did have the right to protest, even if it was over the imaginary idea that they did pay for it.
However all protests at large crowd events, especially large partisan crowd events, will be controlled by various bits of public order legislation that has nothing at all to do with the "class" of those that the spectators are there to spectator.