The answer to why the legislators did not overturn proroguing first before proroguing and then take time to make sure no deal happened has been given in the submission at the Supreme Court, by Aidan O'Neill QC.
He pointed out that a power that rests with the Monarch (and therefore with the Prime Minister) can be legislated against but only after the Monarch has agreed to give up the power. This means the Prime Minister, because the Monarch only acts on advice. So Boris Johnson would have refused to give up the power, and therefore Parliament could not have legislated to bring proroguing under Statute Law.
In the case of the Fixed-term Parliaments Act, the legislation was introduced by the Government and therefore the Prime Minister at the time will have 'advised' that the power was given up. Therefore the Monarch's power on that one was moved into Statute Law, and the Prime Minister lost the exclusive power (in the name of the Monarch) to call a General Election.
Perhaps the next Labour or Liberal Democrat government will bring proroguing under Statute Law and the operation of the legislature, although a difficulty here is that the ceremony is the Monarch inviting the House of Commons to the House of Lords for the proroguing ceremony to take place. It might be in legislation something for the House of Lords to do, but if it did not follow the Commons then the Commons might have the power to overrule it - according to such an Act of Parliament. Only suggesting!